1,120
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Calling Your Own Genome, May 2015 (view source)
Revision as of 11:26, 22 May 2015
, 11:26, 22 May 2015→Extracting only exonic SNPs
And they can be combined as follows
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
(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 ====
==== Exonic Variants NOT found by 1000G ====
