The qc module can take a custom bed file to restrict to loci where the qc metrics will be collected. While using it for external cohorts, I found that sometimes bed files can have uneven number of columns and consist of rows with standard chr\tstart\tend structure + plus other rows with uneven number of annotation columns. This was creating bedtools confusion in the rule _qc_sort_baits, and in turn causing this rule to fail while handling such bedfiles.
This PR adds a step to only process the standard first 3 columns of the bed file, therefore resolving the error.
This update was tested on toy bed files and on real samples in gambl, both tests were behaving as expected and generating the expected bed outputs.
The qc module can take a custom bed file to restrict to loci where the qc metrics will be collected. While using it for external cohorts, I found that sometimes bed files can have uneven number of columns and consist of rows with standard chr\tstart\tend structure + plus other rows with uneven number of annotation columns. This was creating bedtools confusion in the rule
_qc_sort_baits, and in turn causing this rule to fail while handling such bedfiles.This PR adds a step to only process the standard first 3 columns of the bed file, therefore resolving the error.
This update was tested on toy bed files and on real samples in gambl, both tests were behaving as expected and generating the expected bed outputs.