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Revision as of 15:58, 12 December 2014
, 15:58, 12 December 2014→Annotation / Lookup against dbSNP
Looking up SNPs by rsID is possible by (for example)
Looking up SNPs by rsID is possible by (for example)
$HK/vcf-lookup-rsid --vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --sepchr --rs rs17766217
$HK/vcf-lookup-rsid --vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --sepchr --rs rs17766217
* Be sure to look at the QUAL & your sample's PL, and not just the GL field. Check if QUAL is 0 or PL is 0,0,0 - NS is also probably 0; DP is probably 0. That means you probably didn't have any copies, so your GT may not be correct/is unknown.
If you want to browse the rsIDs of known GWAS SNPs, you can do this by
If you want to browse the rsIDs of known GWAS SNPs, you can do this by
