Call variants returns different results for same gene

[tonydisera]

A user noticed that call variants returned more variants after reducing the +/- region. I noticed that we are getting only incomplete headers back for some genes and for other genes, a set of variant records that truncates in the middle of the genotype field.

[tonydisera]

When I launch gene with the crams only for the demo trio, many of the genes return 0 called variants.

https://gene.iobio.io/?gene=BRCA2&genes=ARHGAP8,BRCA1,PDHA1,PLXNA1,RAI1,SCN8A,SMARCA2,BRCA2&species=Human&build=GRCh38&affectedSibs=&unaffectedSibs=&rel0=proband&sex0=female&vcf0=&tbi0=&bam0=https%3A%2F%2Fiobio.s3.amazonaws.com%2Fsamples%2Fcram%2F2021_platinum%2FGRCh38_exomes%2FNA12878.cram&bai0=https%3A%2F%2Fiobio.s3.amazonaws.com%2Fsamples%2Fcram%2F2021_platinum%2FGRCh38_exomes%2FNA12878.cram.crai&sample0=&affectedStatus0=affected&rel1=mother&sex1=female&vcf1=&tbi1=&bam1=https%3A%2F%2Fiobio.s3.amazonaws.com%2Fsamples%2Fcram%2F2021_platinum%2FGRCh38_exomes%2FNA12892.cram&bai1=https%3A%2F%2Fiobio.s3.amazonaws.com%2Fsamples%2Fcram%2F2021_platinum%2FGRCh38_exomes%2FNA12892.cram.crai&sample1=&affectedStatus1=unaffected&rel2=father&sex2=male&vcf2=&tbi2=&bam2=https%3A%2F%2Fiobio.s3.amazonaws.com%2Fsamples%2Fcram%2F2021_platinum%2FGRCh38_exomes%2FNA12891.cram&bai2=https%3A%2F%2Fiobio.s3.amazonaws.com%2Fsamples%2Fcram%2F2021_platinum%2FGRCh38_exomes%2FNA12891.cram.crai&sample2=&affectedStatus2=unaffected

[tonydisera]

Here is the curl:

curl 'https://backend.iobio.io/freebayesJointCallV2' \
  -H 'authority: backend.iobio.io' \
  -H 'accept: */*' \
  -H 'accept-language: en-US,en;q=0.9' \
  -H 'content-type: text/plain; charset=UTF-8' \
  -H 'origin: https://gene.iobio.io' \
  -H 'referer: https://gene.iobio.io/' \
  -H 'sec-ch-ua: "Not/A)Brand";v="99", "Google Chrome";v="115", "Chromium";v="115"' \
  -H 'sec-ch-ua-mobile: ?0' \
  -H 'sec-ch-ua-platform: "macOS"' \
  -H 'sec-fetch-dest: empty' \
  -H 'sec-fetch-mode: cors' \
  -H 'sec-fetch-site: same-site' \
  -H 'user-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/115.0.0.0 Safari/537.36' \
  --data-raw '{"_requestId":"dxdw-idtd","_appendErrors":true,"_attemptNum":1,"alignmentSources":[{"bamUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12878.cram","baiUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12878.cram.crai"},{"bamUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12892.cram","baiUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12892.cram.crai"},{"bamUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12891.cram","baiUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12891.cram.crai"}],"refFastaFile":"./data/references/homo_sapiens/hg38/chr13.fa","region":{"refName":"chr13","start":32314086,"end":32401268},"fbArgs":{"useSuggestedVariants":{"value":true,"defaultValue":true},"limitToSuggestedVariants":{"value":false,"defaultValue":false,"argName":"-l","isFlag":true},"minMappingQual":{"value":0,"defaultValue":0,"argName":"--min-mapping-quality"},"minCoverage":{"value":0,"defaultValue":0,"argName":"--min-coverage"},"useDupReads":{"value":false,"defaultValue":false,"argName":"--use-duplicate-reads","isFlag":true}},"refNames":["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr20","chr21","chr22","chrX","chrY"],"genomeBuildName":"GRCh38","vepREVELFile":"./vep-cache/GRCh38_revel_all_chromosomes_for_vep.tsv.gz","vepAF":true,"isRefSeq":false,"clinvarUrl":"https://backend.iobio.io/static/clinvar/GRCh38/clinvar.vcf.gz","sampleNames":["NA12878","NA12892","NA12891"],"decompose":true}' \
  --compressed

[tonydisera]

curl 'https://backend.iobio.io/freebayesJointCallV2' \
  -H 'authority: backend.iobio.io' \
  -H 'accept: */*' \
  -H 'accept-language: en-US,en;q=0.9' \
  -H 'content-type: text/plain; charset=UTF-8' \
  -H 'origin: https://gene.iobio.io' \
  -H 'referer: https://gene.iobio.io/' \
  -H 'sec-ch-ua: "Not/A)Brand";v="99", "Google Chrome";v="115", "Chromium";v="115"' \
  -H 'sec-ch-ua-mobile: ?0' \
  -H 'sec-ch-ua-platform: "macOS"' \
  -H 'sec-fetch-dest: empty' \
  -H 'sec-fetch-mode: cors' \
  -H 'sec-fetch-site: same-site' \
  -H 'user-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/115.0.0.0 Safari/537.36' \
  --data-raw '{"_requestId":"dxdw-idtd","_appendErrors":true,"_attemptNum":1,"alignmentSources":[{"bamUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12878.cram","baiUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12878.cram.crai"},{"bamUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12892.cram","baiUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12892.cram.crai"},{"bamUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12891.cram","baiUrl":"https://iobio.s3.amazonaws.com/samples/cram/2021_platinum/GRCh38_exomes/NA12891.cram.crai"}],"refFastaFile":"./data/references/homo_sapiens/hg38/chr13.fa","region":{"refName":"chr13","start":32314086,"end":32401268},"fbArgs":{"useSuggestedVariants":{"value":true,"defaultValue":true},"limitToSuggestedVariants":{"value":false,"defaultValue":false,"argName":"-l","isFlag":true},"minMappingQual":{"value":0,"defaultValue":0,"argName":"--min-mapping-quality"},"minCoverage":{"value":0,"defaultValue":0,"argName":"--min-coverage"},"useDupReads":{"value":false,"defaultValue":false,"argName":"--use-duplicate-reads","isFlag":true}},"refNames":["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr20","chr21","chr22","chrX","chrY"],"genomeBuildName":"GRCh38","vepREVELFile":"./vep-cache/GRCh38_revel_all_chromosomes_for_vep.tsv.gz","vepAF":true,"isRefSeq":false,"clinvarUrl":"https://backend.iobio.io/static/clinvar/GRCh38/clinvar.vcf.gz","sampleNames":["NA12878","NA12892","NA12891"],"decompose":true}' \
  --compressed

[tonydisera]

This was actually a case where called variants were being duplicated. See issue #952.