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nikostourvas / acorn_poolseq_pipeline

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grenedalf fails to convert VarScan filtered VCF to sync file #14

Closed nikostourvas closed 12 months ago

nikostourvas commented 1 year ago

This is the VCF that is produced after we remove regions near INDELS. Try converting with the initial VCF that VarScan produces. This is not a big issue because grenedalf can already convert BAM files to sync. However tainted VCF files might lead to issues with other software in the future.

nikostourvas commented 12 months ago

This is caused due to Varscan's unconventional FORMAT field naming scheme in VCF output. Grenedalf expects the AD field to contain read depth for reference and alt allele, but this is not true. A solution is to produce a csv input file with the correct fields for grenedalf.