filter by frequency of heterozygote genotypes #294
Merged
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
|
hi, not to be bothersome, but just checking if there are issues with this pull request, as a few users are now using the associated branch. If there is a problem with merging it into master, I'm happy to keep the branch active and up-to-date. |
|
Hi Very sorry about this, I hadnt seen this pull request, actually I hadnt noticed the other pull requests either. Thanks for poking me. |
|
Hi, to calculate the het, let's say per gene, do I just sum up the per site het frequencies (as output by -minHetFreq -1 -doHWE) across all sites within a gene startpos - endpos, and divide this sum by the total number of sites? |
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Outdated suggestions cannot be applied.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.
Adds
-maxHetFreq <float>and-minHetFreq <float>options to-doHWE. These filter sites on basis of fraction heterozygote genotypes, using maximum likelihood estimates of F/allele freq that are already calculated for HWE test. Min/max filters can be used in tandem, and if either are invoked then the estimated fraction is printed as an additional column tooutput.hwe.gz.This addresses #156, #248, #263 etc that all basically want a simple way to remove/extract collapsed paralogs.