
Hugo DENIS
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Can CalculateGenotypePosteriors be used on hard-filtered VCF
Hi, I was wondering if it is possible/makes sense to use CalculateGenotypePosteriors tool on a hard-filtered multi-sample vcf file ? I have a large multi-sample vcf file (>800 individuals) from a...
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Is it recommended to filter out SNPs around INDELS ?
Hi, thanks a lot for this amazing tool, I have seen in different variant filtration pipelines people recommending to remove/mask SNPs that are located close to INDELs (e.g., 5-10 bp from INDELS po...
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GenotypeGVCFs issue when using --include-non-variant-sites parameter
Hi, I am running similar issues as in this post : https://github.com/broadinstitute/gatk/issues/8415 but I am reposting here as it seems this is a more convenient place to get an answer. I am run...
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GenotypeGVCFs error bgzf_open: Assertion `compressBound(0xff00) < 0x10000' failed.
Dear All: I run a first test of using GenomicsDBImport (version gatk-4.5.0.0 ) to combine 2 gvcf files which worked fine. But when trying to perform joint genotyping a java error is raised. The co...