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Issues with group-expr in Mutect2 VCF

Open fridells51 opened this issue 1 year ago • 0 comments

I am having difficulty getting slivar expressions to show up when using a VCF generated by GATK Mutect2. The command I am using:

./slivar expr --vcf git_sample.txt \
      --alias test.txt \
      -o test.vcf \
      --group-expr 'tumor_normal:(tumors.het && normals.hom_ref)' \
      --group-expr 'tumor_het:(tumors.alts == 1)'

The only time I have ever gotten an expression to work is when i do something like "normals.alts != 0" or "tumors.alts != 0" The variants were decomposed at multiallelic sites using bcftools. Here is the console output: Screen Shot 2022-08-22 at 4 45 11 PM

The group file and sample vcf are attached:

test.txt

git_sample.txt

Thank you for your time.

fridells51 avatar Aug 22 '22 20:08 fridells51