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At the moment, the core haplotype calling algorithm considers only a collection of explicitly designated SNPs. But there is often rare/cryptic variation at non-target sites within the locus. This thre…
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Hello Folks,
Strelka2 is our go to caller for standard somatic variant calling. It works well down to about 5% AF. We'd like it to work with our ctDNA variant calling where the read depth exceeds…
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Hi bcftools team,
I have a conceptual question about mpileup and I think the -d flag is either being weird or I'm misunderstanding how it works. I am using bcftools v. 1.18, and the .bam file in q…
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## Feature request
### Tool(s) or class(es) involved
Many....
### Description
Currently, it is very difficult to split a multiallelic VariantContexts. There are components in GATK that do p…
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# Bug Report
## Affected tool(s) or class(es)
gatk `GenomicsDBImport ` `GenotypeGVCFs`
## Affected version(s)
The Genome Analysis Toolkit (GATK) v4.5.0.0
## Description
Hi,
Here is my situati…
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I am running HATCHet v1.1 (recently upgraded from v1.0) in bioconda. I am having trouble with `count-alleles` generating incomplete output files. I am working within the `hatchet run` pipeline, but ha…
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Hi there. I am trying to generate BAF files using test data and encountering the following error:
Could not find test/1_allele_counts.bin.gz.
The command I used is
mkdir test; samtools view SRR1295…
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Hi Brad,
I am assuming the recall jar uses optimized parameter settings for the variant caller based on bcbio settings. I've been looking at exploring incremental join calling on tumour only samples.…
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When an alternate allele has a length of 0 and there's only 1 alternate allele, the alternate allele field is printed in the VCF as the empty string. While this is technically not incorrect, it causes…
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**Heterozygous genotype with two non-reference alleles**
As [proposed by @nh13 over in another issue](https://github.com/varlociraptor/varlociraptor/issues/153#issuecomment-830391640), this would b…