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AfshinLab / BLR

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Compute phasing stats even when we call our own variants #15

Closed marcelm closed 4 years ago

marcelm commented 4 years ago

I’m opening this small PR to ensure I’m not overlooking something.

The mapped.phasing_stats.(txt|tsv) files are currently only computed when the user has supplied both a ground-truth VCF and a ready-made VCF that contains already called variants (that is, when we don’t do our own variant calling).

However, I would think that we want to compute those stats even if we call our own variants, as long as the ground truth VCF is available.

pontushojer commented 4 years ago

This is definitely possible but it will not output the same stats. To get the error rate the same unphased VCF file has to be used, so for the called variants only half of the stats will be computed.

I think we should perhaps also include stats from whatshap stats. This tool includes stuff like how man variants were phased and other thing that we could have use of. but this could be a separate PR.