sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f61329f36bee18d585b2e2438e93d0a2db384c5754d23127cbd047d13e3fa968 | Shell | 8,211 | 243 | #!/bin/bash
#set -e
NCORE=8
# make top dirs
mkdir -p track
mkdir -p brainmask
mkdir -p wmc
mkdir -p csd
mkdir -p 5tt
# set variables
anat=`jq -r '.anat' config.json`
dtiinit=`jq -r '.dtiinit' config.json`
dwi=$(jq -r .dwi config.json)
bvecs=`jq -r '.bvecs' config.json`
bvals=`jq -r '.bvals' config.json`
mask=`jq -r... |
9783a8c2c5ffa20dc0fdbfa87ac36cb4ae5c7f0120e549621d5b205538ba3168 | Shell | 8,262 | 218 | #!/bin/bash
# 'KAS-Analyzer normalize' was developed by Ruitu Lyu on 12-10-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer normalize [ -h/--help ] [-m methods ] [ -k KAS-seq ] [ -r ratios ] [ -b ] [ -s assembly id ]"
exampleHelp="Examp... |
ce033dd1b4654c2ef548ff34b2fea10e87d449cdc5be78643bd5ed0a9fe2fbf7 | Shell | 8,336 | 195 | #!/bin/bash
#
# This script performs:
# - segmentation of spinal cord from T2w data (seg_sc_contrast_agnostic)
# - detection of PMJ from T2w data (sct_detect_pmj).
# - generation of intervertebral disc labels from T2w data (sct_label_vertebrae)
# - projection of intervertebral disc labels to the spinal cord centerline ... |
e2fb74662ca7e3c86b44d6de2b88130831013afbb9c226d6ee40d826a96a573a | Shell | 8,351 | 224 | #!/bin/bash
# 05_T2w.sh
#This script requires the usage of ANTs N4BiasFieldCorrection.
#We used ANTs version 2.3.1
# What shall be done?
cropAuto=1
biascorrect=1
denoise=1
segment=1
label=1
qc_check=1
#settings
cropA_minX=0
cropA_sizeX=-1
cropA_minY=0
cropA_sizeY=-1
cropA_minZ=0
#loop over subjects
for subject in {... |
ca5a5177bc21697bc5e1e903d6f659dbca0bbd226249f7418e132198855bb163 | Shell | 8,624 | 223 | #!/bin/bash
# 01_DenoiseMocoCombined.sh
# What shall be done
prepData=1
thermnoise=1
moco=1
moco_refined=1
csf_mask=1
# Loop across sessions for data preparation
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub "%02d" $subject
printf -v ses "%02d" $session
echo "subject: " $sub "sessio... |
e08bb09485bd750d791012bdf1cc1637a4e82954c186617086521ddd049f5bda | Shell | 8,652 | 145 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
a7cc2b174bbf4219ad928ee2fa82e094008d09df18fe0ec9231da7f0ad951bfa | Shell | 8,692 | 235 | #!/bin/bash
# run_star <list_of_samples> <J20/Tg4510_input_directory> <output_dir>
# Aim: Individually align RNASeq filtered fastq files to STAR-indexed genome using STAR, and subsequently input SJ.out.bed file into SQANTI2
run_star(){
source activate sqanti2
echo "STAR Version"
STAR --version
# samto... |
d83f900acee12141eee9554e8b85e48b4b781b562b4f92e3f601ac66750cac63 | Shell | 8,745 | 220 | #!/bin/bash
#PatientSpecificMappingAndBinomTest_bowtie2.sh
################################################################################
# The script below was used to map fastqs to the hg38 genome for comparison to
# a mapping to the personalized vg genome.
#
# The script below is tailored to our local com... |
6ee0ba57406250d91af8309b43ce90077e08b588f6e7b28171556b3601950805 | Shell | 8,785 | 158 | #!/bin/bash
image=$1
file=$2
seq 15 +10 20000 > RANGE_x_or
seq 50 +15 20000 > RANGE_or
StartX=$(cat $file | awk -v OFS="\t" '{if (NR >1) print $1}')
EndX=$(cat $file | awk -v OFS="\t" '{if (NR >1) print $2}')
StartX_bottom=$(cat $file | awk -v OFS="\t" '{if (NR >1) print $4}')
EndX_bottom=$(cat $file | awk -v OFS="\t... |
8833cd56f449091a27e655538e6b981f4f65cda24923501a682f4076aa729ecb | Shell | 8,810 | 272 | #!/bin/bash
# Compares per-sample concordance between two SV callsets
set -e
###USAGE
usage(){
cat <<EOF
usage: compare_callsets_perSample.sh [options] SET1.tar.gz SET2.tar.gz SAMPLES CONTIGS OUTDIR
Helper tool to compare the sensitivity of one SV callset vs another
Positional arguments:
SET1.tar.gz ... |
bc292bcb63b527411455b11359d0a0d69bead57a2fb1b2d6f96723a6abacce4f | Shell | 8,839 | 259 | #!/bin/bash
RUN_ID=ichinose_fly_profiling
WORKING_DIR="/datanfs22/${RUN_ID}"
POOL_ID_A=IP
POOL_ID_B=Input
SAMPLE_LIST_A="poolA.csv"
SAMPLE_ID_A=( $(cut -d ',' -f1 ${SAMPLE_LIST_A} ) )
SAMPLE_LIST_B="poolB.csv"
SAMPLE_ID_B=( $(cut -d ',' -f1 ${SAMPLE_LIST_B} ) )
DEPLETION_SOURCE="./190919_Neuro_Glia/genome/fly_ncr... |
2a31fca371b68060cf27f5ca0f97e5b74a01b7228981e9fac9e661f0f9b52c90 | Shell | 8,966 | 200 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
3253f4a86aa0245c87cd5c0c32b3d58f55d3ff6df5795cb0fb1af36be359fec8 | Shell | 9,055 | 260 | #!/bin/bash
#
set -euo pipefail
bed=$1
PE_counts=$2
RD_genotypes=$3
RD_melted_genotypes=$4
RF_cutoffs=$5
blacklist=$6
batch=$7
egrep "DEL|DUP" ${bed} > cnv.bed;
# filter out potential overlapping variants##
bedtools intersect -wa -wb -a cnv.bed -b cnv.bed \
| awk '{if ($4 != $11) print $4"\n"$11}' \
| sort -u \... |
e74458b2d471165990d4a208f00440bb16d8b51e32b278c8ae8ab0decf13ef2c | Shell | 9,079 | 74 | echo ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
echo -e ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Deeplab Modified a1m1 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<"
python3 build_trt.py --weight '/media/Data/ignored/newnet_resnet18_64_newHead_m1_a1/05022022_050501/best_mode... |
f39d674e5cdc012cc88d240e8a65060ddfdbf529ddf23732651490d03fae5b15 | Shell | 9,099 | 133 | #1. methylation level of promoter, utr'5, exon, intron, utr'3 and genebody
#1.1 get the position of each genome feature
#1) promoter (TSS forward 2000bp and TSS downstream 200bp)
# get gene bed information (should keep strand direction information)
cat Sus_scrofa.Sscrofa11.1.98.gtf|awk -v OFS="\t" '$3=="gene"{p... |
01054840d8cc8b82096ea92efc7f66c1adbda9b5914866d36033f1cbe7a88d0a | Shell | 9,219 | 140 | #!/bin/bash
########################## GIMME Input Prep Script ###########################
### The goal of this script for me is to be able to call different sets of commands based on which step I'd like to run. The purpose will be to extract and format the data used in GIMME analysis.
# At this point, you should ha... |
fb837bc8d9e85a176daa057d24cecd97448f0dfdbd570b62eb9b97769251d6d3 | Shell | 9,266 | 245 | #!/bin/bash
# Example:
# sh CBIG_gwMRF_unit_test.sh ~/storage/Temporary/CBIG_gwMRF_unit_test
#
# Written by Yang Qing and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
user=`whoami`
###############################
# Set paths and create log file
#############################... |
9a057c6663ead566310faac25ebe72c83e6e68f5e41f3db13c16dc30a16bdabc | Shell | 9,278 | 241 | #!/bin/bash
#
# SR_genotype.sh
#
set -euo pipefail
vcf=$1
SR_counts=$2
SR_sum=$3
RD_melted_genotypes=$4
RF_cutoffs=$5
whitelist=$6
petrainfile=$7
pegenotypes=$8
batch=$9
sr_pval=$(awk -F'\t' 'NR==1{for(i=1;i<=NF;i++) col[$i]=i; next}
{if ( $col["metric"]=="SRQ") print $col["cutoff"]}' $RF_cutoffs | head ... |
b1fde103136fc3b985cf5e4e2651b421b6365fa29caf1c04a155b38c9b098cdf | Shell | 9,301 | 258 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
e2fe6f27981ed40a2f405153794e46bf49a0fb223d35bbb65af244eec2d5554e | Shell | 9,349 | 313 | #!/bin/bash
PRINT_USAGE () {
echo "Usage $0 [flags] [modules]" >&2;
echo "Valid modules: all, gui, simulator or batch (default is all)" >&2;
echo "Valid flags:" >&2;
echo "-f - force recompilation" >&2;
echo "-l - write build log on compile_commands.json" >&2;
echo "-q - quiet compilation. O... |
33f0d7003b9e6990715769c73cfcda6fe674c744cf2824833588e145ebb79ba9 | Shell | 9,461 | 221 | #!/bin/bash
folder_name=$1
analysis_starting_point=$2
user_name="$USER"
echo $folder_name
# check the folder's log what is the last step completed
step_completed=$(AnalysisProgress.sh $folder_name)
if [ -z "$step_completed" ]; then
# cannot determine the last step completed
step_completed=-1
fi
# if there was no ... |
9786058ae1ba4801033512f3c66f19e0f846fd048a3cf7487dcabef67f2909fe | Shell | 9,475 | 277 | ################################################################################################
# 1) run_QC <sample> <sequencing_summary> <bam_input> <output_dir>
################################################################################################
module load Miniconda2/4.3.21
# 1) run_merge <raw_dire... |
eb05cd6f74dcc42e6bd1da856c98d0841bbcf92e375e66098daa72ad2a2ad2e2 | Shell | 9,499 | 252 | #!/bin/bash
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
function ExcludeIntervalsByEndpoints() {
local _vcf=$1
local _reference_fasta_fai=$2
local _intervals=$3
local _output_prefix=$4
cut -f1,2 "${_reference_fasta_fai}" > genome.file
... |
e6d9f2560b286f6ba0b784dd54c3ea0ea78f0381bb034d3bfa86df2034e4a1fb | Shell | 9,531 | 194 | #!/bin/bash
# 'KAS-Analyzer SST_enhancer' was developed by Ruitu Lyu on 1-22-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer SST_enhancer [ -h/--help ] [ -o prefix ] [ -t threads ] [ -s assembly id ] [ -e enhancer ] [ -p peaks ] [ -k KAS-seq ] "
exampleHelp="Example: nohup KAS-Analyzer SS... |
954bf30fbac6fd256777ce72e5edf4f76f2777006d162db99d85f97d52bb6698 | Shell | 9,612 | 200 | #!/bin/bash
# 'KAS-Analyzer genomicdist' was developed by Ruitu Lyu on 12-12-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer genomicdist [ -h/--help ] [ -o prefix ] [ -c ] [ -p peaks ] [ -s assembly id ]"
exampleHelp="Example: nohup KAS-Analyzer genomicdist -o KAS-seq_genomic_distribution... |
757af65798fd0928d459f447d9b51aa58adce429f670fcb35cd391a2427b8222 | Shell | 9,767 | 318 | #!/bin/bash
# Collects QC data for SV VCF output by SV pipeline
set -e
###USAGE
usage(){
cat <<EOF
usage: collectQC.sh [-h] [-F FAM] [-R] VCF SVTYPES BENCHDIR OUTDIR
Helper tool to collect QC data for a VCF output by sv-pipeline
Positional arguments:
VCF VCF from sv-pipeline
SVTYPES List o... |
b9c31c05b9db887be2c0f01b84c63ac255843e83a15d351ca31e74600dc85f5a | Shell | 9,779 | 230 | #!/bin/bash
# Benchmarks the sensitivity of one SV callset against another
set -e
###USAGE
usage(){
cat <<EOF
usage: compare_callsets.sh [options] SET1 SET2
Helper tool to compare the sensitivity of one SV callset vs another
Positional arguments:
SET1 SV callset to be benchmarked
SET2 Gr... |
a29130033d15e8afe9aba615f85effbf722089f4bcaca729e96231239999082f | Shell | 9,863 | 263 | #!/bin/bash
# Benchmarks the sensitivity of one SV callset against another
set -e
###USAGE
usage(){
cat <<EOF
usage: compare_callsets.sh [options] SET1 SET2 CONTIGS
Helper tool to compare the sensitivity of one SV callset vs another
Positional arguments:
SET1 SV callset to be benchmarked
SET2 ... |
64d01d6a6bec863fd392fbb34ac9b55a0e4af02db307e1220cd0addb82acb4ff | Shell | 9,992 | 261 | #!/bin/bash
set -Exeuo pipefail
function ShardBedThenConvertToVcf()
{
local _del_or_dup=$1
local _bed=$2
local -n vcfs_array=$3
local -n vcfs_idx_array=$4
cd "${working_dir}"
# Task: ScatterCompressedBedOmitHeaders
shard_bed_convert_vcf_working_dir=$(mktemp -d ${SV_SHELL_BASE_DIR}/wd_shard_bed_convert... |
f2ccff1bb3650b065cfffbba12d2d84c30cf86991b53a7c42b2c4dd502bc24bd | Shell | 10,177 | 217 | #!/bin/bash
#
# The script performs inter-rater variability analysis across subjects
# Namely:
# - segment spinal cord (using SCT)
# - detect PMJ label (using SCT)
# - copy ground truth rootlets segmentation (located under derivatives/labels)
# - segment rootlets (using our nnUNet model)
# - run 02a_rootlets_... |
1f5805b6d8e8c3913c56815d023f6f44a2dea9a80bd00a9f54f15e40307a704e | Shell | 10,186 | 156 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
#... |
0ae77e6df76c9d5247ae9c7fd846c519c2c194a49c293c3be4d5ab9bdf85545e | Shell | 10,190 | 263 | #!/bin/bash
set -Exeuo pipefail
function BedtoolsClosest()
{
local _bed_a=$1
local _bed_b=$2
local _out=$3
paste <(head -1 "${_bed_a}") <(head -1 "${_bed_b}") | sed -e "s/#//g" > "${_out}"
bedtools closest -wo -a <(sort -k1,1 -k2,2n "${_bed_a}") -b <(sort -k1,1 -k2,2n "${_bed_b}") >> "${_out}"
}
# -------... |
70433f01c2d59609871eb2a8098b01a4732197192c488d5720f275adbcdfb8e3 | Shell | 10,200 | 154 | #!/bin/bash
#SBATCH -c 1
#SBATCH -p normal
#SBATCH --mem=64g
#SBATCH --time=12:00:00
export PATH=~/omiicsTransfer/software/bedtools2/bin/:$PATH
# v2 improves intron definition by using ucsc table browser introns and intron retention is now only searched in bsj spanning reads, not all reads as before
sample=$1
org... |
52b7567d98001214a92b0b189b5222727e268943c92b3c16bfb391a6d152b71d | Shell | 10,203 | 273 | #!/bin/bash
# 'KAS-Analyzer saturation' was developed by Ruitu Lyu on 12-16-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer saturation [ -h/--help ] [ -o prefix ] [ -s assembly id ] [ -c control ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-Analyzer saturation -o KAS-seq_saturation -s... |
d0c73341c92eca51de6126253edb0ef0172ef91662fa5e486f8b5030612474e1 | Shell | 10,308 | 299 | # source functions
LOGEN_ROOT=/gpfs/mrc0/projects/Research_Project-MRC148213/sl693/scripts/LOGen
FICLE_ROOT=/gpfs/mrc0/projects/Research_Project-MRC148213/sl693/scripts/FICLE
export PATH=$PATH:${LOGEN_ROOT}/target_gene_annotation
export PATH=$PATH:${LOGEN_ROOT}/merge_characterise_dataset
export PATH=$PATH:${FICLE_ROOT}... |
c8a1f93795287b74db364c8e303940f32cb544271d72bb761bf13725afd54fad | Shell | 10,387 | 365 | #!/bin/bash
##########################################################
##########################################################
# FUNCTIONS
log()
{
local msg="$*"
local dateTime=`date`
echo "# "$dateTime "-" $log_toolName "-" "$msg"
echo "$msg"
echo
}
#########################################... |
d4d0d9caad410153178a3eefa55b81eb4a37013131a0a45b4dfe1150a1f59df8 | Shell | 10,428 | 176 | #!/bin/bash
# The "qmri-ald" program provides automated image-processing pipelines for
# structural MRI images primarily acquired in pediatric healthy controls
# and pediatric patients with cerebral adrenoleukodystrophy. The program
# provides preprocessing, processing, quantitative, and statistical analysis
# of MRI i... |
9a8d3e93fe60e81a177cf484055fda522cb3c46fc05381ff339eacd4d2113eef | Shell | 10,445 | 243 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
31ab1a5056ae93a9a651f08fa878532216538a2bc75f39f94c2af028bb9d0e4e | Shell | 10,498 | 176 | # Data from an Asthma GWAS called gabriel
# Note https://beaune.cng.fr/gabriel/gabriel_results_description.xls is a description of the columns
wget https://beaune.cng.fr/gabriel/gabriel_results.zip
unzip gabriel_results.zip
rm gabriel_results.zip
mv gabriel_asthma_meta-analysis_36studies_format_repository_NEJM.txt gabr... |
5a5abae63c23a321ace3af343304119b68dc889d0499125f8a13aac57f93ab0b | Shell | 10,541 | 249 | #!/bin/bash
#
##########################
# define a helper function
##########################
warn_msg () {
# only output warning msg when the shell is interactive
if [[ $- == *i* ]]; then
echo $1
fi
}
####################################################
# export paths for subdirectories of CBIG repositor... |
eddd214c32714f4d1df8867dbc8a4891e94728caaf88a8341d42a4f6b6810953 | Shell | 10,655 | 246 | #!/bin/bash
# 'KAS-Analyzer download' was developped by Ruitu Lyu on 12-01-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer download [ -l ] [ -h ] [ -a aligner ] [ -g assembly id ] [ -d directory to save index of aligner ]"
exampleHelp=... |
ebcd48687de33cca977339a9b69b0010e62b43167167883a1e2fce622ae4dbeb | Shell | 10,707 | 199 | ##---------------------------------------##
# ATAC-Seq data analysis
##---------------------------------------##
##------------------------------------------------------ Based on original genome -------------------------------------------------
##1)The statistics of raw sequencing data
while read line
... |
d53918a58b5dd41e051862c272cf606a63f26fb8f122505953889ad7f3b59abb | Shell | 10,840 | 112 |
# Format in the runall.sh script
# coaccessCut=$1 # Cicero co-accessibility cutoff to count
# maxSites=$2 # Max number of sites to link
# peakSize=$3 # Size of distal sites
# upstream=$4
# downstream=$5
# 9-13-21
# Test sending off batch submissions this way
qsub -l mfree=20G -wd /net/trapnell/vol1/h... |
0633c197cc7c3250ec830fc5038dba93c6f7154c32da5345ed128d77f77297ea | Shell | 11,155 | 252 | #!/bin/bash
set -Exeuo pipefail
function get_seeded_random() {
SEED="$1"
openssl enc -aes-256-ctr -pass pass:"$SEED" -nosalt </dev/zero 2>/dev/null
}
function run_gcnv_case() {
java "-Xmx${JVM_MAX_MEM}" -jar /opt/gatk.jar GermlineCNVCaller \
--run-mode CASE \
--arguments_file read_count_files.args \
... |
a70049dc4dc9c40e55e56b82d1db9c189d38132a540adfda00cbfb2852ddac66 | Shell | 11,209 | 263 | #!/usr/bin/env bash
#
# This is a script to process DRUG-seq reads. It is a modified version of
# Drop-seq_alignment.sh provided alongside of Dropseqtools from Steve McCarroll's lab.
#
# Author: Rebekka Wegmann, Snijder lab, ETH Zurich
# Original version Copyright 2017 Broad Institute
#
# MIT License
#
#
# Permission... |
8b6e88f3223df0609d75b179b47c47465ad93ab36c8f67ccf4245b6b396a295c | Shell | 11,326 | 284 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
2fc658828494da8eadab4567841b6da9c9594bf57abfe8f3dd6c940587a7ea90 | Shell | 11,347 | 284 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
033daf6d819ce4c54159278a40c551cb06f5a0ebed7a849f7bd35f97201873a6 | Shell | 11,373 | 312 | #!/bin/bash
set -Exeuo pipefail
function getJavaMem() {
# get JVM memory in MiB by getting total memory from /proc/meminfo
# and multiplying by java_mem_fraction
local mem_fraction=${java_mem_fraction:=0.85}
cat /proc/meminfo | \
awk -v MEM_FIELD="$1" -v frac="${mem_fraction}" '{
f[substr($1, 1, l... |
e9d9789c9c8f5463bbb95a9342c79cd93890a001f3e36d5b769e8c6264ef503a | Shell | 11,495 | 286 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
a1583c8f2a87f4c64e24413abb2496a93aa68a6516fbdd278b0cb84eec46c54b | Shell | 11,559 | 286 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
c4e7858ac9200366eb6336c3e27f3be5bfbdb1457769c1ad1fcaf30cdabc2966 | Shell | 11,612 | 286 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
1b31c4bcaec3debbe701f49430aff03a336338736044881f04f3a0d1bd165535 | Shell | 11,616 | 286 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
b3a2941645806e606ba5ab9c61307fe4cd21a45eb81fbf59c0d4ce52da648ce6 | Shell | 11,639 | 248 | #!/bin/bash
# 'KAS-Analyzer SST_enhancer' was developed by Ruitu Lyu on 1-22-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer SST_enhancer [ -h/--help ] [ -o prefix ] [ -t threads ] [ -s assembly id ] [ -e enhancer ] [ -p peaks ] [ -k KAS-seq ] "
exampleHelp="Example: nohup KAS-Analyzer SS... |
566b75c6dc2347b46c8fa9afb4d675ea5e733f56aa88a0293c4315b2293239c6 | Shell | 11,680 | 286 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
ef323e970cc561ef0aacd91748495c5a89673c23d1eaf086730e51be5bda127c | Shell | 11,691 | 286 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
b9c1ee11e3a152fa74d89d35bc483acd2fc677981ae178459b49dd2eaf819da2 | Shell | 11,739 | 284 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
35335104a23f2efcf155abaf8f6fe73cff70e506c5b11c8352ac8d47462cb78e | Shell | 11,747 | 379 | #!/bin/bash
SCRIPTNAME=$(basename $0)
USAGESTR="
NAME
${SCRIPTNAME} Does GLM hyperparameter grid search and GLM fitting for a single cell type.
SYNOPSIS
${SCRIPTNAME} <fit_type> <config> <cell_type> <output_base> [optional one-letter arguments]
OPTIONS
-j <jitter-sd> Standard deviation of Gaussian for pert... |
dad3749c4e948d979bc0af51493971c04c3762206c3161c14d077dab4cf1599c | Shell | 11,834 | 432 | #!/bin/bash
#SBATCH -J postcap_seedfree
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=8
#SBATCH --partition=day
#SBATCH --time=1-00:00:00
#SBATCH --output="/CAP_Time_Analytics/time-analytics/slurm_output/postcap_seedfree-%A.out"
module load miniconda
source activate pycap_env
#################################... |
c9ccd28ccdd76e002ac324c33671dbfe16e97f0afed1185178a4accb9985914a | Shell | 11,944 | 418 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Nicolas Servant, Eric Viara
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD-3 licence.
## See the LICENCE file for details
## This script aims ... |
bebb3cc09951d2d1b29a877de7501237ccbc25b032d0c4645bb9b9de7790d9c1 | Shell | 12,005 | 284 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
5da2c31dff74d77429a7968494fe54916b38a4fa9e70e0588ece91e73c456408 | Shell | 12,051 | 289 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
16890d14781c77b0a6fd4be4ba43a7147bc6a52026a012b8bfa925d6f503fd61 | Shell | 12,269 | 299 | #!/bin/bash
#
# SR_genotype.sh
#
set -euo pipefail
##Genotype##
function assign_genotype_quality () {
# Arguments
INFILE=$1
VIDS_LIST=$2
MEDIAN_HET=$3
STDEV=$4
GQ_FILE=$5
VARQ_FILE=$6
##normalization factor##
##Normalize phred scores to 999 if count is the mean ##
normalization=$(Rscript -e "pr... |
19a7b92891d820ad6116d120dc021987f62b29b5e30a8fb38566ae5ebd24cfe1 | Shell | 12,377 | 286 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
2f967f49bca763202da9559adfbb9b1c2b1d761ab99666bce874a8a958f2badd | Shell | 12,511 | 270 | #!/bin/bash
# 'KAS-Analyzer termilength' was developed by Ruitu Lyu on 1-25-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer termilength [ -h/--help ] [ -o prefix ] [ -t threads ] [ -b bin size ] [ -g assembly id ] [ -p peaks ] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-... |
67e9f3abf72835ae99e77e07154311f7b35d31045d04f7206b234f83c3938504 | Shell | 12,528 | 263 | #!/bin/bash
# Loop through all directories matching the pattern
for dir in /ZPOOL/data/projects/SRPAL-DataInBrief/bids/sub-*/func/; do
# Extract the subject ID from the directory path
sub_id=$(basename $(dirname "$dir"))
# Create the events JSON file for each task and run
for task in trust sociald... |
0108cf2b06c18c0ce32b88105c48045508e7bebb2cb9095290cf4562083f7ce8 | Shell | 12,624 | 289 | #
# gccopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with gcc 3.2.3.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after running mex. N... |
0b666ffcec4a899793a4d7656a1dfdb6d72f9d1c258e6007db10b11ab14b6129 | Shell | 12,753 | 324 | #!/bin/bash
#
# SR_genotype.sh
#
set -euo pipefail
vcf=$1
SR_counts=$2
SR_sum=$3
RD_melted_genotypes=$4
RF_cutoffs=$5
whitelist=$6
petrainfile=$7
pegenotypes=$8
sr_pval=$( awk -F'\t' '{if ( $5=="SRQ") print $2}' $RF_cutoffs | head -n 1)
sr_count=$(/opt/sv-pipeline/04_variant_resolution/scripts/convert_poisson_p.py... |
cf1e532f1167a23f0f0a500ba7556f32bfb20221f51cd53e3ad5d9227eb6ed6d | Shell | 13,045 | 381 | #!/usr/bin/env bash
# Push caller's shell options (quietly)
{ SHELLOPTS_STACK="${SHELLOPTS_STACK-}|$(set +o); set -$-"; } 2> /dev/null
set -eo pipefail
if [ -z "${TRAVIS_PULL_REQUEST-}" ] || [ -n "${OSTYPE##darwin*}" ]; then set -ux; fi
ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE:-$0}")"; pwd)"
WORKSPACE_DIR="${ROOT_DI... |
f7d42c7bf5a4116726b380b42603b243c9cd9978a90fa008d06c024a67086781 | Shell | 13,449 | 348 | #
# mexopts.sh Shell script for configuring MEX-file creation script,
# mex. These options were tested with the specified compiler.
#
# usage: Do not call this file directly; it is sourced by the
# mex shell script. Modify only if you don't like the
# defaults after ru... |
5d25770ff3ac6bf1a874ebf41cd0020ba4e5d424ad38f6c086250ec1838418b3 | Shell | 13,791 | 335 | #!/bin/bash
# 'KAS-Analyzer peakscalling' was developed by Ruitu Lyu on 12-09-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer peakscalling [ -h ] [ -m peaks caller ] [ -t KAS-seq ] [ -c Control ] [ -b mode ] [ -o prefix ] [ -p pvalue o... |
3a5b4d75fd7f65e40aa789913af5ce5371b60bfc11f9050a4e98ee26893e4f62 | Shell | 14,134 | 354 | #!/bin/bash
# 'KAS-Analyzer correlation' was developed by Ruitu Lyu on 12-10-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer correlation [ -h/--help ] [ -m correlation method ] [ -t threads ] [ -s assembly id ] [ -r regions ] [ -f peak... |
d7583b06fd2d24a0ce06ad2ef10d46b4a146efaebdb0494507631605ee9c3f43 | Shell | 14,150 | 104 |
# 2-7-22: Run regression by cell type to find cell-type spec motifs, adding UMI to the
qsub -P trapnelllab -l mfree=80G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_05_redoPeakMotifRegression_nobackup/ /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_05_redoPeakMotifRegressi... |
d9f7d7167fc10b5cf9dac57294b38bad74b11222727e93450bd924f2e7099795 | Shell | 14,667 | 398 | #!/bin/bash
#
# IntegrateGQ.sh
#
set -euo pipefail
vcf=$1
RD_melted_genotypes=$2
RD_melted_variants_gentoypes=$3
pegeno_indiv_file=$4
pegeno_variants_file=$5
srgeno_indiv_file=$6
srgeno_variants_file=$7
#Final Output for individual genotype file VID IID RD-Geno, RD-GQ, PE-Geno, PE-GQ, SR-Geno, SR-GQ, Combined-Geno... |
c3749a7abc41c568ba90e1aee08fa767a3e1949120233fce023141d4a8e064d2 | Shell | 14,742 | 364 | #!/bin/bash
set -Exeuo pipefail
function SeekDepthSuppForCpx()
{
local _cpx_lg_cnv=$1
local _raw_depth_bed=$2
local _prefix=$3
zcat "${_cpx_lg_cnv}" | awk '{print $6}' | sort | uniq > sample_list.tsv
echo -e '#chr\tpos\tend\tSVTYPE\tSVID\tsample\tbatch\tdepth_cov' > "${_prefix}.depth_supp.bed"
while re... |
ff22f2cd8fecfa9a3f333e43b3ab1a2c15eff685ee8e8fff236f10ecf6e8c4af | Shell | 15,267 | 336 | #!/bin/bash
# 'KAS-Analyzer PCA' was developed by Ruitu Lyu on 12-16-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer PCA [ -h/--help ] [ -o prefix ] [ -t threads ] [ -r regions ] [ -s assembly id ] [ -b bin size ] [ -p peaks] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-A... |
be979e9182354276bfcef7c0bff6f0c53f27a79ad7ae1c6aa10ca344895ccacd | Shell | 15,743 | 310 | #!/bin/bash
# 'KAS-Analyzer index' was developed by Ruitu Lyu on 1-22-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer index [ -h/--help ] [ -o prefix ] [ -t threads ] [ -s assembly id ] [ -i index types ] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-Analyzer index -o KAS-... |
ccbaa7d8968618d6e0959e8ccde838b7f394a3efbb18be94a61c6457d5e3962c | Shell | 15,778 | 403 | #!/bin/bash
# 'KAS-Analyzer correlation' was developed by Ruitu Lyu on 12-10-2021.
# Stop on error
set -e
## Read arguments
usageHelp="Usage: KAS-Analyzer correlation [ -h/--help ] [ -m correlation method ] [ -t threads ] [ -s assembly id ] [ -r regions ] [ -f peak... |
e01a714aa785a1d009ff10a9707ea70dac3b3074f1e82173b724720d25e13ff1 | Shell | 15,818 | 381 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
11fd352a0af95a0a7cd245a93b0cc33caa73de554548f0b88a963884e3c04f97 | Shell | 16,089 | 317 | #! /bin/bash
# ============================================================
# pipeline script for processing fastq to gvcf
# ============================================================
# get command line options
# ============================================================
args=`getopt -o "r:,d:,t:,o:,s:,b:" -l "r... |
5a0f822ac6beb9e3c1fec13992c841e4c03b7eb97bbaeea65564658e8e3ac3b1 | Shell | 16,527 | 280 | #!/bin/bash
#run592 /Data/2c7dycd7ut/UnalignedL1/Project_PAAC_L1_H1401P_Ciernia
#run590 /Data/xfm70hwv8e/UnL6L7/Project_PAAC_H1401P_Ciernia
#run590 /Data/49bxhv50b5/UnL6L7/Project_PAAC_H1401P_Ciernia
#######################################################################################
#RNA QuantSeq Analysis: https... |
f957986fbff5051ff07e5a15efb68ccc4a47e1588e048dc0b44e2e471ae226cd | Shell | 16,589 | 149 |
qsub -P trapnelllab -l mfree=10G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_19_largeScaleMixedModeling_nobackup/ /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_19_largeScaleMixedModeling_nobackup/singleMMrun.sh Endocardium
qsub -P trapnelllab -l mfree=10G -wd /net/trapnell/... |
145a2cd1ec7919c8cf6b12b54f98e3f1b9c2423148bcd8b8907cc8426921f956 | Shell | 16,700 | 440 | # Szi Kay Leung (sl693@exeter.ac.uk)
################################################################################################
## Define functions for <Sample>_Nanopore.sh
# 1) run_merge <input_fasta_dir> <sample_output_name>
# 2) run_nanofilt <sample_output_name_merged.fastq> <sample_output_name> <root_dir>
# 3... |
25ca9b18d69931f75c6f614173b14f372d5d3f259d0123b052da692d295f4c51 | Shell | 16,836 | 403 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
7c6c0e81741e772a218e8fdba1edc6f673ccd75280a7009eba796c48a63933c3 | Shell | 16,933 | 457 | #!/usr/bin/env bash
# Push caller's shell options (quietly)
{ SHELLOPTS_STACK="${SHELLOPTS_STACK-}|$(set +o); set -$-"; } 2> /dev/null
set -euxo pipefail
SCRIPT_DIR=$(builtin cd "$(dirname "${BASH_SOURCE:-$0}")"; pwd)
WORKSPACE_DIR="${SCRIPT_DIR}/../.."
# importing install_miniforge function
source "${SCRIPT_DIR}/i... |
95d6a778378ae8c92a62d21de16225e5f5448c25fd7eda761f726b109fad8ac7 | Shell | 17,020 | 389 | #!/bin/bash
# 'KAS-Analyzer PCA' was developed by Ruitu Lyu on 12-16-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer PCA [ -h/--help ] [ -o prefix ] [ -t threads ] [ -r regions ] [ -s assembly id ] [ -b bin size ] [ -p peaks] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-A... |
a38fc16ce93d38ea91d07b1a9b0541ce0c17f30a0dda523f055a40f89c22a8c8 | Shell | 17,075 | 358 | #!/bin/bash
# 'KAS-Analyzer index' was developed by Ruitu Lyu on 1-22-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer index [ -h/--help ] [ -o prefix ] [ -t threads ] [ -s assembly id ] [ -i index types ] [ -l labels ] [ -k KAS-seq ]"
exampleHelp="Example: nohup KAS-Analyzer index -o KAS-... |
e727a6fc39deca80d947cf47142ae394c1ae74c0329dc0eedd2f4f32b8d84ef6 | Shell | 17,968 | 399 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if ... |
ebba450ac27ab67f00478b29ffb41a5275bd493d91f89aa6912532e57193a33f | Shell | 18,010 | 415 | #!/bin/bash
##### FSL v5.0 #####
## Create expansion maps from baboon cross species registration using fslmaths ##
## This script should be run in code dir that is then the relative path = ../data/deformations/
## from the deformation and T1 images. This can be changed by adapting $data_dir ##
## The inputs are the... |
9bb7bff172980bfeff40fc9c3af16ff0630faaa4efc65d25d1a7f2347c142f6a | Shell | 18,156 | 352 | #!/bin/bash
# 'KAS-Analyzer KASindex' was developed by Ruitu Lyu on 1-19-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer KASindex [ -h/--help ] [ -t threads ] [ -o prefix ] [ -s assembly id ] [ -r regions ] [ -p peaks ] [ -l labels ] [ -k KAS-seq ] "
exampleHelp="Example: nohup KAS-Analyz... |
44ba0baff5590a7eee5d4d8a1909cff7e1aa687347145a3f2be8ec7afb7d9f49 | Shell | 18,213 | 350 | #!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified April 12, 2018
Description: Compares reads to the kmers in a reference dataset, optionally
allowing an edit distance. Splits the reads into two outputs - those that
match the reference, and those that don't. Can also trim (remove) the matching
pa... |
ba488bcf5138c0de86b0cbfec43c51904e759b1ca17183cbce93fb777fd7e2fd | Shell | 18,312 | 353 | #1)Add read group information #
#=============================#
for sample in DB1 DB2 DB3 DB4 DS2 DS3 DS4 LB1 LB2 LB3 LB4 LS1 LS2 LS3 LS4
do
file1="$sample"_R1.fq.gz
file2="$sample"_R2.fq.gz
mkdir $sample
sbatch --time=24:00:00 --export=dir=$sample,file1=$file1,file2=$file2 --output=$sample/fq.split.out ... |
8702437e11d30e3afd873f383f35d2c69a55f16c0ce9ba7f1daa1bdcdae52223 | Shell | 19,003 | 435 | #!/bin/bash
################################################################################################
## Define functions for All_Tg4510_Functions.sh
# 1) run_CCS <input_ccs_bam> <prefix_output_name> <Output_directory>
# 2) run_LIMA $Sample $Input_CCS_directory $Output_directory <"no_multiplex"/"multiplex">
# 3)... |
227a38bd689ddc6d20321c19002bde618132ca3e8bf20b7fa02944629722f1aa | Shell | 19,573 | 675 | #!/bin/bash
<<'COMMENT'
josh faskowitz
Indiana University
Computational Cognitive Neurosciene Lab
Copyright (c) 2018 Josh Faskowitz
See LICENSE file for license
COMMENT
####################################################################
####################################################################
#
# This s... |
4f23bc030c06d2cb22ce63f71756ec08889b0a5e66e6efae1078ccdbd48ae714 | Shell | 19,885 | 467 | #!/bin/bash
set -e
umask u+rw,g+rw # give group read/write permissions to all new files
dataset=$1
subj=$2
step_name=$3
task=$4
subj_list=$5
if [[ -z "$task" ]] ; then
task='FH'
fi
if [[ -z "$subj_list" ]] ; then
subj_list=''
fi
origdir=/vols/Data/sj/Nicole/${dataset}
SD=$origdir/derivatives
sdir=/vols/Scrat... |
29f087dc1177b631deaf29e38985ee4390bab61d93af516a39e376d7883046d8 | Shell | 20,299 | 421 | #!/bin/bash
# 'KAS-Analyzer KASindex' was developed by Ruitu Lyu on 1-19-2022.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer KASindex [ -h/--help ] [ -t threads ] [ -o prefix ] [ -s assembly id ] [ -r regions ] [ -p peaks ] [ -l labels ] [ -k KAS-seq ] "
exampleHelp="Example: nohup KAS-Analyz... |
16d9e1d62353ed8af1e5dec0b56ff1ac581871c71f00192379a647c98ccc0370 | Shell | 20,495 | 482 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
c5ca3d8b6658056118be2e5436ecb1cac84d655d73a7bbfb4a29761363045a32 | Shell | 20,559 | 415 | #!/bin/bash
# 'KAS-Analyzer profile' was developed by Ruitu Lyu on 12-14-2021.
# Stop on error
set -e
# help arguments
usageHelp="Usage: KAS-Analyzer profile [ -h/--help ] [ -t threads ] [ -s assembly id ] [ -e length ] [ -o prefix ] [ -r regions ] [ -p peaks file ] [ -f peaks files list ] [ -l labels ] [ -c colors ]... |
5cb532aca8050870564cc6bd006db1854bdd174caff827b46eb0dc2f6ac3f7c1 | Shell | 20,978 | 514 | #!/bin/bash
# For details: https://serverfault.com/a/103569
# saves original stdout to &3 and original stderr to &4
# without this, the logs of subprocess can get mixed with the parent's logs.
exec 3>&1 4>&2
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=tru... |
4f7b17af48ec142a446f0667dc716e26b3c5cc830f2597c1591612e98425100f | Shell | 21,544 | 293 | #-------------------------------------------------------------------------------
# A_Orginal Genome #
#-------------------------------------------------------------------------------
#0. combine the fastq files from two pairs to one pair,so that we can us... |
0b31bd19b10fdfb9a4ad76f9619bcaac414472bf23c1d9555429a4fc8c633dad | Shell | 22,788 | 310 | #!/bin/bash
set -e
##SR##
mkdir $wrkdir/SR
##require to pass both initial RD and BAF to be considered valid and fail both to be invalid###
##remove events as failing that have potential PE support##
fgrep -w -f <(awk '{print $1}' $wrkdir/BAF/BAF.d*.metrics) \
<(cat $wrkdir/BAF/BAF.del.pred $wrkdir/BAF/BAF.dup.pr... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.