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Hello,
I am trying to use the TOPMed Variant Calling Pipeline (latest: Freeze 8) to analyze human genetic data from 651 exome sequencing samples. I am following the instructions on the Readme (https:…
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Hi Thierry,
I'm running into issues with Radiator when running filter_rad() using a VCF file generated through Stacks. Additionally, my colleagues (who are running Radiator on MAC-OS) also run into…
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Dear GenoCAE maintainer,
Thanks for the conversion of the example files to PLINK format! I checked the .bim and .fam file and they match the PLINK doc (this time, I checked more carefully :-) ).
…
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Hi,
I'm trying to use PureCN 1.20.0 from conda (I installed the missing package r-optparse from conda).
My vcf file is the output of gatk FilterMutectCalls on gatk Mutect2 (--genotype-germline-sit…
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there have different result when I use all two sample together or only use one of two samples to call variants.
the one sample code is "bcftools mpileup -Ou sample1.bam -f ref.fa | bcftools call -mv…
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Hi @fritzsedlazeck,
first of all thanks for the great set of tools!
I've been following your Wiki page on SV calling for a population and I've run into an issue.
The final merged GTF contains the…
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Hello, I was hoping you could explain the differences between each of the options you can use for the `--variant_caller` option. How do each of these differ in terms of the type of model produced and …
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View details in Rollbar: [https://rollbar.com/jimmy.andrews/VariantGrid/items/2366/](https://rollbar.com/jimmy.andrews/VariantGrid/items/2366/)
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UploadPipeline 3862 failed. Filename: Clinvar Error…
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Hello,
I have VCF file with merged allele counts and frequencies from different subsets (gnomad V.3.1 genomes).
In the INFO field, there are AC, AN, and AF values given for all set; and then, AC, AN…
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Hi,
Is it possible to build a reference using MHC alleles from other species? I have the allele sequences, and I wonder which files should I modify in arcasHLA/dat/.
Thanks