Mcall #389
Merged
Mcall #389
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
…m in bcftools, implemented for comparison purposes
… to ensure ordering of alt alleles. This code will like be removed at a later point
…tput is still diallelic. Need to think about how to represent things. Maybe just an integer from 0-9 similar to the offset of the gl arrays
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Outdated suggestions cannot be applied.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.
For comparison purposes I added the multiallelic caller described in this document:
https://samtools.github.io/bcftools/call-m.pdf
For now it only outputs the diallelic genotype calls. At some point Ill add everything. I just need to figure out the best representation for these multiallelic calls. Currently everything in ANGSD is flipped according to major minor or reference centric with the -domajorminor option. Maybe a single char[5] array where the first one is the reference, not sure yet.