Add in frequency based functionalities of NgsRelate (and add allele frequencies as a targeted output as a byproduct) #52
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
…r ngsrelate with ibsrelate method only. This also pars down the output to only the usable columns with the frequency free method.
This adds in the ability to polarize population Beagles/MAFs to either their within pop major allele or the within dataset allele.
|
Pruning before NgsRelate is removed in the previous commit. This is because, as per the ngsrelate v2 paper, the composite likelihood generated when including linked sites should still have consistent with the unlinked likelihood estimates, and so pruning shouldn't be needed generally. If at some point this is good to have it can be added back in. |
As I was trying to add mafs as a targetable output, the way I handled polarization of major/minor seemed needlessy complicated. Instead, maf can just be done separately in a single rule or two and it cuts down on complexity a lot.
This time with less complicated maf calcs. If this works, targeting mafs, and the subsequent polarization requirements that has, will be added in another PR.
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Outdated suggestions cannot be applied.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.
Previously the inclusion of NgsRelate in the workflow largely was to offer a SNP based way to do the IBSrelate method. However, with allele frequencies it can also co-estimate inbreeding and relatedness. This PR will add the ability to choose between using the IBSrelate method in NgsRelate only, or also using the frequency based methods. This will utilize the same population level Beagle rules as ngsF-HMM, but will take the MAF files, requiring a bit more care in their generation, so they probably can be added as a targeted output afterwards.
Closes #49.