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How To Prepare Gatk .Vcf Files Output For Annovar ?

I have managed to generate vcf files by using bwa + PiCard + GATK pipeline, and would like to use ANNOVAR to do the variant calling. I checked the vcf content output from GATK, and think it is not ready for feeding into ANNOVAR. I was wondering if there's any handy tool to prepare the GATK vcf files for ANNOVAR? thanks for reply

variant calling gatk annovar vcf
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updated by Ram Ram • written by newDNASeqer newDNASeqer

2 answers

From the ANNOVAR manual:

perl convert2annovar.pl infile.vcf -format vcf4 > outfile

As an aside, I think you are slightly confused when you say use ANNOVAR to do "variant calling". What you have in your vcf file are variants that were called using GATK. ANNOVAR does ANNOtation of VARiants by either locating interrupted or closest genomic features (genes, transcription factors, etc.) or filtering the variants based on another set of variant genotypes you supply.

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updated by Ram Ram • written by Matt Shirley Matt Shirley

Thank you for your answer, appreciate it.

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written by newDNASeqer newDNASeqer

Also, is there any way to convert the Annovar file (containing INDELs info) to vcf file (using hg19 as ref genome).

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updated by Ram Ram • written by amitgsir amitgsir

For those who find this 8 years later...

table_annovar.pl takes vcf input directly with the --vcfinput argument.

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updated by Ram Ram • written by sander.debacker • sander.debacker

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