To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

SelectVariants -env doesn't remove all non-variant sites

I am using GATKv3.7, trying to remove a few samples from a big VCF file and remove all invariant sites. Here is the code I ran:

java -jar GenomeAnalysisTK-3.7-0/GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V 142_samples.vcf -xl_sn TC050 -xl_sn TC052 -xl_sn TC054 -xl_sn TC056 -xl_sn TC059 -xl_sn TC060 -xl_sn TC060_09.05 -xl_sn TC062 -xl_sn TCDH29 -xl_sn TCViera -xl_sn TCy -env -o 131_samples.vcf

I use the -env tag, and the header of the resulting VCF does indeed say "Exclude non-variant Sites = true", and while it did remove a lot of the sites that the excluded samples were variant for, I still have many invariant sites in the file (about 20K invariant and 10K variant). Is there a way to remove these invariant sites directly from the VCF using your tools? I can remove them easily from fasta down the line, but I'm not a competent enough coder to modify VCF files like this.

Thanks!

Alex

Best Answer

Answers

Sign In or Register to comment.