This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how do I create vcf4.1 instead of 4.2

I just created a vcf file for multiple genomes using the following command below, but it generates vcf4.2 version. I am using a tool that only accepts 4.1 version. Is there a way to downgrade a vcf file to 4.1. Also, what options do I need to change to create vcf4.1 in GATK?

java -Xmx58g -Djava.io.tmpdir=$SCRATCH  -jar $GATK/GenomeAnalysisTK.jar  \
-R $GENOME/UCSC_ALL_FULL_CHROMS_HG19.fasta  \
-nt 10 \
-T UnifiedGenotyper \
vcf
• 5,785 views • link
updated by igor igor • written by MAPK MAPK

vcftools perl modules have a tool vcf-convert . Not tried it for downgrading though.

• 1 views • link
written by microfuge microfuge

1 answer

As far as I know, you can't adjust VCF version in GATK. However, 4.1 and 4.2 are not that different. You may be able to manually adjust the files so they fit your requirement. It's just a text file.

For example, GATK HaplotypeCaller (version 3.4) is producing a VCF that is supposed to be 4.2, but defining the AD field as "Number=." (VCF 4.1 specification) rather than "Number=R" (VCF 4.2 specification). I end up fixing that because another tool complained about it.

You should consult the GATK forums for GATK-related questions, which are closely monitored by GATK staff: http://gatkforums.broadinstitute.org/gatk

• 1 views • link
written by igor igor

Log in to answer this question.

More posts like this