I've been wasting a lot of time lately by manually running vcf normalization commands. This PR adds two normalization steps to the pipeline:
bcftools norm -f: On by default, but can be toggled in the config XML
vcfwave: Toggle on with --vcfwave (this will output an additional VCF that has bee n vcfwave-normalized in addition to the usual output)
Because I couldn't figure out how to make a static vcfwave binary, I'm only including it in the Docker release for now. There's a hopefully-helpful error checker to help users work around this.
I've been wasting a lot of time lately by manually running vcf normalization commands. This PR adds two normalization steps to the pipeline:
bcftools norm -f: On by default, but can be toggled in the config XMLvcfwave: Toggle on with--vcfwave(this will output an additional VCF that has bee nvcfwave-normalized in addition to the usual output)Because I couldn't figure out how to make a static
vcfwavebinary, I'm only including it in the Docker release for now. There's a hopefully-helpful error checker to help users work around this.