addresses the issue by modifying the CallVariants step to use the -L and -d parameters to improve sensitivity for INDELS in the output .vcf files.
passes the quality threshold that was used for CallConsensus to also be used in CallVariants consistent with recent changes upstream in the CZB sc2 pipeline.
This was tested offline using a sample with a known INDEL. The pipeline previously did not output the corresponding lines in the .vcf file, but the change has resulted in successful identification of the known INDEL.
A recent issue was raised that we were missing some INDEL calls in the output .vcf files https://github.com/chanzuckerberg/idseq-workflows/issues/97
This PR does the following:
CallVariants
step to use the-L
and-d
parameters to improve sensitivity for INDELS in the output .vcf files.CallConsensus
to also be used inCallVariants
consistent with recent changes upstream in the CZB sc2 pipeline.This was tested offline using a sample with a known INDEL. The pipeline previously did not output the corresponding lines in the .vcf file, but the change has resulted in successful identification of the known INDEL.