| set -uo pipefail |
| module load bcftools/1.16 >/dev/null 2>&1 |
| R=/ibex/project/c2041/hany0c/bench_h2h_20260915/real |
| V=$R/raw/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz |
| echo "start $(date -u +%FT%TZ) host $(hostname)" |
| echo "== GT values chr2:10000000-10100000 (all 3202 samples)" |
| bcftools query -r chr2:10000000-10100000 -f "[%GT\n]" $V 2>/dev/null | sort | uniq -c |
| echo "== samples VCF vs ped" |
| bcftools query -l $V > $R/logs/.vcf_samples.tmp |
| awk "NR>1{print \$2}" $R/ref/20130606_g1k_3202_samples_ped_population.txt | sort > $R/logs/.ped_samples.tmp |
| sort $R/logs/.vcf_samples.tmp | comm -3 - $R/logs/.ped_samples.tmp | wc -l |
| rm -f $R/logs/.vcf_samples.tmp $R/logs/.ped_samples.tmp |
| echo "== whole-file site scan (no genotypes)" |
| bcftools query -f "%POS\t%FILTER\t%TYPE\t%N_ALT\t%INFO/AC\n" $V 2>/dev/null | awk -F"\t" " |
| {n++; filt[\$2]++; typ[\$3]++; |
| if(\$3==\"snp\" && \$4==1){bs++; if(\$5==1)ac1++; if(\$5<mn||mn==\"\")mn=\$5; pc[\$1]++} |
| if(\$3==\"snp\") snpany[\$1]++} |
| END{print \"records\",n; for(k in filt)print \"FILTER\",k,filt[k]; for(k in typ)print \"TYPE\",k,typ[k]; |
| print \"biallelic_snv\",bs,\"AC_min\",mn,\"AC==1\",ac1+0; |
| d=0; dr=0; for(p in pc) if(pc[p]>1){d++; dr+=pc[p]}; print \"biallelic_snv positions with >1 biallelic snv record\",d,\"records\",dr; |
| e=0; for(p in snpany) if(snpany[p]>1)e++; print \"positions with >1 SNV record (any N_ALT)\",e}" |
| echo "end $(date -u +%FT%TZ)" |
|
|
