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broadinstitute / tgg_methods

Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
MIT License
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Address sample callrate filtering #13

Open mike-w-wilson opened 4 years ago

mike-w-wilson commented 4 years ago

The current seqr sample qc pipeline does not apply hard filters in the get_qc_mt function: https://github.com/broadinstitute/gnomad_methods/blob/0b8e1007aacabcb81e4093d9e315ac6f7c92651b/gnomad/sample_qc/pipeline.py#L106 . Should we add it in as the UKBB does? We also do not flag internal exomes for low callrate.

gtiao commented 4 years ago

I think it's a good idea to flag these, although I don't think the seqr sample QC function should remove samples that fail hard filters. We should flag internal exomes for low callrate.

G.

On Thu, Jun 4, 2020 at 3:57 PM Mike Wilson notifications@github.com wrote:

The current seqr sample qc pipeline does not apply hard filters in the get_qc_mt function: https://github.com/broadinstitute/gnomad_methods/blob/0b8e1007aacabcb81e4093d9e315ac6f7c92651b/gnomad/sample_qc/pipeline.py#L106 . Should we add it in as the UKBB does? We also do not flag internal exomes for low callrate.

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