VariantFiltration filtering all SNPs for all samples to missing

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Wiebe Kooistra

• December 04, 2023 08:38

REQUIRED for all errors and issues:
a) GATK version used: 4.4.0.0
b) Exact command used:

        gatk VariantFiltration -R ${reference} -V ${vcf} \

        --genotype-filter-name 'GQ_20' --genotype-filter-expression "GQ<10" \

        --genotype-filter-name 'RGQ_20' --genotype-filter-expression "RGQ<10" \

        --set-filtered-genotype-to-no-call --output ${sample}.vcf

 

Hi,

I am using VariantFiltration to filter out SNPs that have a value lower then 10. What I see happening is that rows that do not have GQ in their FORMAT are also filtered and put to no-call. Is this the expected behavior? I would expect that the rows that do not have GQ in their FORMAT that they are skipped and stay the same value as they should be.

Thanks in advance.

Wiebe

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  Laura Gauthier

  • January 08, 2024 21:16

  Hi Wiebe Kooistra,

  Given that there is an optional argument `missing-values-evaluate-as-failing` to turn on the behavior of filtering out missing values, no I do not think this is expected behavior.  I'll ask the team to take a look.

  -Laura

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  Wiebe Kooistra

  • February 16, 2024 09:06

  Hey Laura Gauthier

  Thanks for looking into this :).

  Wiebe

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