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Issues with group-expr in Mutect2 VCF
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:
The group file and sample vcf are attached:
Thank you for your time.