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SeqShop: Calling Your Own Genome, May 2015

1 byte removed, 10:26, 22 May 2015
Extracting only exonic SNPs
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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