Attention:
The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

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.