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SeqShop: Calling Your Own Genome, May 2015

12 bytes added, 09:20, 22 May 2015
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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
$HK/run-command-wgs make --cmd "$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)
Or you can run multiple chromosomes in parallel in one command
$HK/run-command-wgs make --cmd "$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 ====

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