| set -uo pipefail | |
| module load bcftools/1.16 >/dev/null 2>&1 | |
| R=/ibex/project/c2041/hany0c/bench_h2h_20260915/real | |
| V=$R/raw/1kGP_high_coverage_Illumina.chr2.filtered.SNV_INDEL_SV_phased_panel.vcf.gz | |
| S=$R/derived/.samples_afr_eur_eas.partial.txt | |
| echo "start $(date -u +%FT%TZ) host $(hostname)" | |
| bcftools view -r chr2:10000000-25000000 -m2 -M2 -v snps -i "INFO/AC<=40" -s $(paste -sd, $S) $V 2>/dev/null \ | |
| | bcftools query -f "%CHROM\t%POS\t%INFO/AC_AFR\t%INFO/AC_AFR_unrel\t%INFO/AC_EUR\t%INFO/AC_EUR_unrel\t%INFO/AC_EAS\t%INFO/AC_EAS_unrel[\t%GT]\n" 2>/dev/null \ | |
| | python3 -B $R/scripts/derive_unrel.py $R/ref/20130606_g1k_3202_samples_ped_population.txt $S $R/derived/.unrel_membership.partial.tsv | |
| echo "end $(date -u +%FT%TZ)" | |