VariantFiltration: Invalid argument value '=='

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

Hi,

My problem is that the VariantFiltration command fails with the -G_filter terms.

My input is:
GenomeAnalysisTK -R ${my_ref} \
-T VariantFiltration -V my_genos.vcf \
-G_filter "isNoCall == 0 || isHomVar == 0" \
-G_filterName "badgenos" \
--invalidatePreviousFilters \
-o dodgey_genos_marked.vcf

The error messages are:
ERROR A USER ERROR has occurred (version 3.4-46-gbc02625):
ERROR MESSAGE: Invalid argument value '==' at position 8.
ERROR Invalid argument value '0' at position 9.
ERROR Invalid argument value '||' at position 10.
ERROR Invalid argument value 'isHomVar' at position 11.
ERROR Invalid argument value '==' at position 12.
ERROR Invalid argument value '0' at position 13.

I've remade the input vcf and idx files (with GATK) so there should be no issue there (as reported in other posts). I've successfully performed a VariantFiltration followed by SelectVariants earlier in the pipeline using another vcf as a mask. --FilterExpression also generates similar error messages.

I was hoping that it's a problem with my syntax but I can't find any mistakes. Do you know of a solution?

Sincerely,

Will

Issue · Github
by Sheila

Issue Number
142
State
open
Last Updated

Best Answer

Answers

Sign In or Register to comment.