Suggestions to calculate variants per sample in exomes and genomes #577
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KoalaQin
commented
Mar 9, 2024
| :param agg_rare_variants: Stratify by variants which have adj AF <0.1%. | ||
| :param suffix: String of arguments to append to name. | ||
| :param pass_filters: Filter to variants which pass all variant qc filters. | ||
| :param ukb_regions: Filter to variants in UKB regions. |
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I'm thinking if all these should be under pass_filters, like:
if pass_filters:
arg_dict.update({"pass_filters": hl.len(vmt.filters) == 0})
if ukb_regions:
....
KoalaQin
changed the title
KoalaQin
commented
Mar 10, 2024
| vmt_vep = vep.filter_vep_transcript_csqs( | ||
| vmt, | ||
| if by_csqs: | ||
| ht = filter_vep_transcript_csqs( |
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Did you or Julia agree on filtering to only MANE select transcripts? I leave it the same for now.
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no, that was just the default. Let me parametrize this in the coming review though
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@matren395 Back to you now! |
matren395
reviewed
Mar 11, 2024
|
@matren395 Back to you again, I deleted two unnecessary arguments and implemented your suggetions (thanks a lot!). New test run: 6776707a23c948d79e9df883d5c4d42f |
matren395
approved these changes
Mar 12, 2024
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I simplified the two functions and renamed a few things, I added in option to get the count of missense and synonymous variants. I also prefer to write the aggregated stats in the HT globals, I think it's better structured this way. We'll discuss if only output just one final HT, but make it two steps.
I got the same number of all_variants the same as you for 1 sample, but number of variants passing filters are not again the same, I think the new Exome release seems changed, we need to confirm with Julia for that.
My test run is here: bcd45e3f472b4033bfac9532a022dafe