Export sites only vcf STEP 1-- 317 add AC, AN, AF to the final VCF #7279
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
RoriCremer
changed the title
RoriCremer
force-pushed
the
rc-317-addACANAF
branch
from
2a914f9 to
605fa54
Compare
kcibul
reviewed
Jun 1, 2021
| @@ -33,6 +33,8 @@ | |||
| import java.util.*; | |||
| import java.util.stream.Collectors; | |||
|
|
|||
| import static htsjdk.variant.variantcontext.VariantContextUtils.calculateChromosomeCounts; | |||
There was a problem hiding this comment.
I find static imports a bit hard to follow in the code, not sure what the GATK style is though (but I haven't seen it very often)
| // add AC/AF/AD annotations | ||
| Set<String> founderIds = new HashSet<>(); | ||
| Map<String, Object> attributes = new HashMap<>(vc.getAttributes()); | ||
| Map<String, Object> chromosomeCounts = calculateChromosomeCounts(vc, attributes, true, founderIds); |
There was a problem hiding this comment.
I think there's a form of this call that doesn't take the last parameter, might bel more clear
| Set<String> founderIds = new HashSet<>(); | ||
| Map<String, Object> attributes = new HashMap<>(vc.getAttributes()); | ||
| Map<String, Object> chromosomeCounts = calculateChromosomeCounts(vc, attributes, true, founderIds); | ||
| builder.putAttributes(chromosomeCounts); |
There was a problem hiding this comment.
the docs on this are confusing (about removing stale attributes, why we pass things in and out, etc) so I'm not sure we need to call putAttribues here...
but the bigger question would be, why not just use the GATK annotation infrastructure?
RoriCremer
force-pushed
the
rc-317-addACANAF
branch
from
8a50a8a to
00996c3
Compare
This was referenced Mar 17, 2023
Closed
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.
So... AC, AN and AF annotations are back in the final VCF.
A few things to note:
These do not respect the FT tag---working with Louis and Laura to make that happen since Louis feels the change will have to happen in htsjdk itself (specifically in the getCalledChrCount method in VariantContext and its different versions)
This solution doesn't pass in any founderIds--likely I'm just missing where they should get pulled from? I assume there are people in AoU that are related? Or is that way outside the scope of any of this?
We may want to add a boolean to make the sites-only VCF require less cleanup from the user.
example is from manually running:
./gatk --java-options "-Xmx9g" ExtractCohort --mode GENOMES --ref-version 38 -R "/Users/aurora/projects/references/hg38/v0/Homo_sapiens_assembly38.fasta" -O "addannotations.vcf.gz" --local-sort-max-records-in-ram 10000000 --sample-table "spec-ops-aou.anvil_100_for_testing.sample_info" --project-id "spec-ops-aou" --cohort-extract-table "spec-ops-aou.anvil_100_for_testing.Rori_Test" -L chr20:1-1000000