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SeqShop: Calling Your Own Genome, May 2015

64 bytes added, 12:10, 22 May 2015
Annotation / Lookup against dbSNP
export EPACTS=/net/seqshop-server/home/mktrost/seqshop/epacts/
export REF=/net/seqshop-server/home/mktrost/seqshop/singleSample/ref/gotcloud.ref
export GC=~/seqshop/gotcloud
 
export SAMPLE=SampleXX
If you want to run this command across all chromosomes in parallel, you can use the special script run-command-wgs
$HK/run-make --repeat-chr --cmd "$HK/vcf-add-rsid -vcf $OUT/vcfs/chr1/chr1.filtered.vcf.gz --db $HK/../data/dbsnp_142.b37.vcf.gz --out $OUT/vcfs/chr1/chr1.filtered.rsid.vcf.gz" --numjobs 6 --out runmake.rsid --autosomes
Looking up SNPs by rsID is possible by (for example, rs17766217) -- How can we find its position?
$HK/tabix ~/NA12878/output$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.
And they can be combined as follows
(zcat $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz; zcat $OUT/vcfs/chr[2-9]/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chr??/chr*.filtered.rsid.anno.exon.vcf.gz $OUT/vcfs/chrX/chrX.filtered.rsid.anno.exon.vcf.gz | grep -v ^#) | $HK/bgzip -c > $OUT/wgs.filtered.rsid.anno.exon.vcf.gz
$HK/tabix -pvcf $OUT/wgs.filtered.rsid.anno.exon.vcf.gz
==== Exonic Variants NOT found by 1000G ====

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