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Revision as of 12:10, 22 May 2015
, 12:10, 22 May 2015→Annotation / Lookup against dbSNP
Looking up SNPs by rsID is possible by (for example, rs17766217) -- How can we find its position?
Looking up SNPs by rsID is possible by (for example, rs17766217) -- How can we find its position?
$HK/tabix ~/NA12878/output/vcfs/chr8/chr8.filtered.rsid.vcf.gz 8:128504497 | less
$HK/tabix $OUT/vcfs/chr8/chr8.filtered.rsid.vcf.gz 8:128504497 | less
* 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.
* 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.
