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Annotating Tabix Indexed Vcf

I would like to annotate a tabix indexed vcf. Thus, my input is a tabix file and my output should also be a tabix file. How can this be accomplished?

vcf tabix
• 5,474 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by rickyflintoff • rickyflintoff

1 answer

unzip your vcf, annotate it, sort, compress with bgzip and re-index with tabix.

gunzip -c yourfile.vcf.gz > tmp1.vcf
annotatetool1  tmp1.vcf > tmp2.vcf
annotatetool2  tmp2.vcf > tmp3.vcf
vcf-sort <  tmp3.vcf |  bgzip -c > annot.vcf.gz
tabix -p vcf annot.vcf.gz

If your tools use stdin and stdout, almost all the command lines below can fit into one pipeline

gunzip -c yourfile.vcf.gz | annotatetool1 | annotatetool2 |  vcf-sort |  bgzip -c >  annot.vcf.gz &&   tabix -p vcf annot.vcf.gz
• 48 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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