Export sites only vcf STEP 1-- 317 add AC, AN, AF to the final VCF #7279
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RoriCremer
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kcibul
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Jun 1, 2021
| @@ -33,6 +33,8 @@ | |||
| import java.util.*; | |||
| import java.util.stream.Collectors; | |||
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| import static htsjdk.variant.variantcontext.VariantContextUtils.calculateChromosomeCounts; | |||
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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); |
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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); |
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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?
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This was referenced Mar 17, 2023
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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