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If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs
If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs
$HK/run-command-wgs --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --numjobs 6
$HK/run-make --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbSNP.b138/dbsnp_138.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --repeat-chr --numjobs 6
Looking up SNPs by rsID is possible by (for example)
Looking up SNPs by rsID is possible by (for example)
Or you can run multiple chromosomes in parallel in one command
Or you can run multiple chromosomes in parallel in one command
$HK/run-command-wgs --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --numjobs 6
$HK/run-make --cmd "$EPACTS/bin/epacts anno --in $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz" --repeat-chr --numjobs 6
==== Extracting only exonic SNPs ====
==== Extracting only exonic SNPs ====
