Fixed handling of allele depths for Indels called by Strelka #215
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Fixed handling of alternate and reference allele depths. Currently, only the variant allele depth (from TIR) is translated to MAF. However, the information for the reference allele is similarly located in TAR, which is now extracted as well. Compare Strelka's updated README: https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Somatic indels: tier1RefCounts = First comma-delimited value from FORMAT/TAR tier1AltCounts = First comma-delimited value from FORMAT/TIR Somatic allele freqeuncy is $tier1AltCounts / ($tier1AltCounts + $tier1RefCounts)
ckandoth
reviewed
Mar 10, 2019
| @depths = map{""} @alleles; | ||
| $depths[0] = ( split /,/, $fmt_info{TAR} )[0]; | ||
| $depths[$var_allele_idx] = ( split /,/, $fmt_info{TIR} )[0]; | ||
|
|
There was a problem hiding this comment.
Missing a closing bracket } here. But otherwise looks good. Thanks for the PR!
5b4013c to
0b91d65
Compare
|
I will merge this into |
This was referenced Oct 9, 2019
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixed handling of alternate and reference allele depths. Currently, only the variant allele depth (from TIR) is translated to MAF. However, the information for the reference allele is similarly located in TAR, which is now extracted as well.
Compare Strelka's updated README: https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic
Somatic indels:
tier1RefCounts = First comma-delimited value from FORMAT/TAR
tier1AltCounts = First comma-delimited value from FORMAT/TIR
Somatic allele freqeuncy is $tier1AltCounts / ($tier1AltCounts + $tier1RefCounts)