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We should create the functionality to do germline calls without tumor genotyping.
This is a backburner issue, but something to think about.
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since i'm converting liftover in these pipelines to scatter/gathers in order to facilitate the ability to perform concordance with either grch37 or 38 genotyping arrays. i should do the gather on the …
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Hi,
Has anyone tried Demuxlet on single nuclei using 10x? Does it work?
Also, what are people using for genotyping of human samples?
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I have called a bunch of samples with straglr and merged the (chrom, start, end, motif) beds into one unified bed. I would like to use this merged bed to genotype each sample again. Sometimes differen…
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Hi,
I have bulk RNA-seq data for each of my human samples, plus the scRNA-seq data that I would like to demultiplex with Vireo. Could I just clarify the workflow?
1. Genotype bulk RNA-seq sample…
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Hi,
I wonder how the genotypes of the parents are corrected using the progeny allele counts. I guess with "correct_variant_types()", in offspringscoring.py? What I find strange is that on my VCFs s…
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It would be nice to add a vignette that goes from reading in data from a VCF file to genotyping and filtering SNPs.
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Hi, I am running octopus with this command in order to genotype a given set of sites:
```
octopus --threads 12 --ignore-unmapped-contigs \
--config ../octopus/resources/configs/PacBioCCS.confi…
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e.g. B2M, TAP, &c.
Identifying loss in MHC might require running a custom program which first does genotyping of the germline MHC and then calls somatic variants against those specific alleles.
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Hi @hannespetur,
We ran graphtyper2 using v2.5.1 two years ago to re-genotype SVs.
We noticed that vcf_merge in v2.5.1 does not include the --sv parameter.
Can we still merge the SVs across samp…