Maximum alt alleles guardrail [VS-1530] #9033
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gbggrant
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Nov 5, 2024
| @@ -135,9 +135,9 @@ Once the VAT table is created and a tsv is exported, the AoU research workbench | |||
| - Specify the same `call_set_identifier`, `dataset_name`, `project_id`, `extract_table_prefix`, and `interval_list` that were used in the `GvsPrepareRangesCallset` run documented above. | |||
| - Specify the `interval_weights_bed` appropriate for the PGEN / VCF extraction run you are performing. `gs://gvs_quickstart_storage/weights/gvs_full_vet_weights_1kb_padded_orig.bed` is the interval weights BED used for Quickstart. | |||
| - For both `GvsExtractCallset` and `GvsExtractCallsetPgenMerged`, select the workflow option "Retry with more memory" and choose a "Memory retry factor" of 1.5 | |||
| - `GvsExtractCallset` currently defaults to 1000 alt alleles maximum, which means that any sites having more than that number of alt alleles will be dropped. Make sure to specify the appropriate `maximum_alternate_alleles` value (currently 100). | |||
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I'm confused. "currently 100?"
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This is carried over from line 140. The value of max alt alleles we were told to use for Echo was 100, but in my testing we seem to be able to go to 1000 at least without WeightedSplitIntervals breaking down. I don't know if variants with > 100 alt alleles are actually useful though.
mcovarr
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Extract and WeightedSplitIntervals don't deal well with arbitrarily large numbers of alt alleles, so add an (overridable) guardrail of 1000 alt alleles max if the user neglects to specify the 100 alt alleles max recommended in our documentation for AoU callsets.