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Illumina / gvcfgenotyper

A utility for merging and genotyping Illumina-style GVCFs.
Apache License 2.0
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Flag FILTER only with "." #18

Closed Talo07 closed 1 year ago

Talo07 commented 1 year ago

Hi, After using gvcfgenotyper on the results of strelka (last version), in the flag filter I find only "." I cannot find for example, the PASS and the other criteria... knowing that in the gvcf of each genome there is this information. How I could have them in the final combined vcf?? Thanks !!

olest commented 1 year ago

Hi @Talo07 , we don't set the FILTER column in the multi-sample VCF output. That is why it is always set to missing "."

Talo07 commented 1 year ago

Thanks @olest for your reply. We would like to filter based on PASS filter, do you have a suggestion?

olest commented 1 year ago

hi @Talo07 , I would recommend using the bcftools plugin fill-tags (https://samtools.github.io/bcftools/howtos/plugin.fill-tags.html) to annotate your multi-sample VCF and then use some of these metrics for filtering. The Inbreeding coefficient, Genotype missingness and read depth are good criteria to filter on.