About SelectVariants

I want to filter out the variants if VAF in tumor samples was more than 0.3.

Command line:
gatk SelectVariants
-V somatic_twofiltered.vcf
-R ucsc.hg19.fasta
-select 'vc.getGenotype("SAMN06041278").getAF()>0.3'
-O somatic_thrfiltered.vcf

Error message: Invalid JEXL expression detected for select-0

I changed the command line as:
gatk SelectVariants
-V somatic_twofiltered.vcf
-R ucsc.hg19.fasta
-select 'vc.getGenotype("SAMN06041278").getAF>0.3'
-O somatic_thrfiltered.vcf

No error, but the new generated vcf only include header, no any variant record.

please help me address this questions!

Tagged:

Answers

Sign In or Register to comment.