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sigven / vcf2tsvpy

Genomic VCF to tab-separated values
MIT License
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Added ability to provide genotype field data when no GT record is present #1

Closed LukeGoodsell closed 6 years ago

LukeGoodsell commented 6 years ago

The script currently won't output any calls if a GT field is not present and the skip_genotype_data flag is not set.

When making somatic calls, some callers (e.g. Strelka) don't include a GT field in the genotype data column. The genotype still contains useful sample-specific data, though.

This change will cause the script to still output the genotype data even when no GT field is present, and the GT field will consist of only "./." values.

sigven commented 6 years ago

Thanks a lot, very good point. I am well aware of the Strelka case, in which the genotype column do not follow any conventions.