Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Moving up ability to set mismatch quality related filter thresholds to the input YAML #169

Open
wants to merge 1 commit into
base: main
Choose a base branch
from

Conversation

ksinghal28
Copy link
Member

Moving up the max_mm_qualsum_diff and max_var_mm_qualsum arguments used by the fpfilter through the following WDLs.
somatic_exome_nonhuman.wdl
detect_variants_nonhuman.wdl
subworkflows/mutect.wdl
subworkflows/strelka_and_post_processing.wdl
subworkflows/varscan_pre_and_post_processing.wdl
subworkflows/fp_filter.wdl
tools/fp_filter.wdl

Noticed that we needed this functionality for a situation where we didn't have a matched normal (as is often the case for non-human experiments), and were not calling a real KRAS G12 variant due to (germline) mismatches in the positions around the variant resulting in us failing variants with flags MMQSD50 and MMQS100 set by the max_mm_qualsum_diff and max_var_mm_qualsum thresholds.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant