Question: How To Prepare Gatk .Vcf Files Output For Annovar ?
1
gravatar for newDNASeqer
6.3 years ago by
newDNASeqer650
United States
newDNASeqer650 wrote:

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

vcf gatk calling variant annovar • 4.0k views
ADD COMMENTlink modified 6.3 years ago by Malachi Griffith17k • written 6.3 years ago by newDNASeqer650
3
gravatar for Matt Shirley
6.3 years ago by
Matt Shirley9.1k
Cambridge, MA
Matt Shirley9.1k wrote:

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.

ADD COMMENTlink modified 14 days ago by RamRS24k • written 6.3 years ago by Matt Shirley9.1k

Thank you for your answer, appreciate it.

ADD REPLYlink written 6.3 years ago by newDNASeqer650

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

ADD REPLYlink written 4.5 years ago by amitgsir50
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