how do I create vcf4.1 instead of 4.2

Question

[MAPK]

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 \

[microfuge]

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

Answer 1

[igor]

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