genotyping calls don't align with coverage

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Gertjan Wils

• March 15, 2022 12:57

Question:

When performing a genotyping I found a difference between the presented genotype and the coverage of the alleles. For example: genotype was called to be 0/0 (homozygous wild type), but the coverage on the reference and alternative allele was almost identical, suggesting heterozygous mutant. Is there a reason why the genotypes are called in this way?

 

REQUIRED for all errors and issues:
a) GATK version used:

GATK/3.5-Java-1.8.0_74 
b) Exact command used:

java -Xmx6G -jar ${EBROOTGATK}/GenomeAnalysisTK.jar -T HaplotypeCaller -R /scratch/gent/vo/000/gvo00027/genomes/homo_sapiens/homo_sapiens_Ensembl_90_38/homo_sapiens_Ensembl_90_38 -I /scratch/gent/vo/000/gvo00027/projects/pxlence/sample_id_comparison/run_113/nimagen//analyses/NA24385D2.rg.sorted.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 -o /scratch/gent/vo/000/gvo00027/projects/pxlence/sample_id_comparison/run_113/nimagen//analyses/NA24385D2.vcf -L samples.txt --emitRefConfidence BP_RESOLUTIO

 
c) Entire program log:

Not applicable

1

• 

  Genevieve Brandt (she/her)

  • March 16, 2022 17:33

  Hi Gertjan Wils,

  Our support team no longer supports GATK3. We recommend that you update to GATK4 because many of the GATK3 bugs are fixed, with also an added benefit that we will help out with questions that you have! 

  See our support policy for more details: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines#support_policy

  Best,

  Genevieve

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