Open fridells51 opened 2 years ago
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:
test.txt
git_sample.txt
Thank you for your time.
I am having difficulty getting slivar expressions to show up when using a VCF generated by GATK Mutect2. The command I am using:
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:
test.txt
git_sample.txt
Thank you for your time.