Using SelectVariants to output "PASS" records
Posted in Ask the GATK team | Last updated on 2013-01-07 20:10:14


Comments (3)

I have completed filtering my SNP data using VariantFiltration, and now I want to use SelectVariants to output all calls marked "PASS" in the FILTER field. I used the following script, but only the header information writes to the output file.

java -Xmx20g -jar GenomeAnalysisTK.jar -T SelectVariants -R HC.fa --variant HC.SNPs.filtered.vcf -select "FILTER == 'PASS'" -o HC.SNPs.passed.vcf

My input file contains many records that should evaluate as true. Any idea why this doesn't this work?


Return to top Comment on this article in the forum