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Additionally, Qualimap results are meant to be at the sample level, but are currently at the Library level. We need to use post-Library-merge BAMs as input for this module.
The additional complication is that MERGE_LIBRARIES currently runs on the BAMs specified by genotyping_source, but other modules probably should run on the raw ones. Maybe always merge the raw ones and only merge trimmed/pmd/rescaled when asked? Then the raw merged sample-level bams can go to Qualimap.
This might also apply to BEDTOOLS_COVERAGE, though I am not entirely sure. @aidaanva ?
The text was updated successfully, but these errors were encountered:
Yes, BEDTOOLS_COVERAGE should run on raw merged ones since the user may want to run those with mapping quality 0, which will not be appropriate for genotyping.
Qualimap needs an
ext.prefix
.Additionally, Qualimap results are meant to be at the sample level, but are currently at the Library level. We need to use post-Library-merge BAMs as input for this module.
The additional complication is that
MERGE_LIBRARIES
currently runs on the BAMs specified bygenotyping_source
, but other modules probably should run on the raw ones. Maybe always merge the raw ones and only merge trimmed/pmd/rescaled when asked? Then the raw merged sample-level bams can go to Qualimap.This might also apply to BEDTOOLS_COVERAGE, though I am not entirely sure. @aidaanva ?
The text was updated successfully, but these errors were encountered: