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Currently `ReferenceConfidenceVariantContextMerger.merge()` does not pass in the remapped alleles to `GATKVariantContextUtils.makeGenotypeCall()` for the `originalGT` argument, which seems problemati…
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Good day,
We are about to start using souporcell as the main tool to demux our single cell data, for which we also have genotyping information.
It turns out that using --commonvariants provides bett…
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A user rightly [points out](http://gatkforums.broadinstitute.org/gatk/discussion/comment/32631#Comment_32631) that different versions of HaplotypeCaller may produce GVCFs that are not directly compati…
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We would like to verify whether there is a significant difference in efficiency of the hm pipeline for seq GWAS.
1. Calculate the average % of dropped and unable to harmonise variants among a repres…
ljwh2 updated
2 months ago
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Filters to implement:
- Sex check based on the input/headers of genotyping-files
- Making sure it's properly read by plink with the VCF
- Genotyping inputs:
- Duplicate variant checks (per…
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Hello --
Thank you for developing and maintaining a powerful resource for the genomics community.
I've genotyped SVs for a species of bird, and noticed there was an aberrantly large inversion t…
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Greetings. Thank you for developing Geny to expand the potential of the KIR genotyping with next-generation sequencing data!
In your manuscript, you also compared the accuracy with T1K, and I appr…
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### Description of feature
Some software, like PureCN, expects to have germline sites called along with somatic sites when using MuTect 2. However, currently there's no way to set `--genotype-germlin…
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Hi,
I have suggestions for "OBI:0000435" - "genotyping assay" term and some of the terms under it.
"Genotyping assay" has synonyms that include snp, which is limiting and confusing, so I'd remo…
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Hi, I found the pangenie-index calculate the unique kmers in the variant flank sequences, so could you please tell me what the unique kmers are used for pangenie genotyping?