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## Feature request
### Tool(s) or class(es) involved
Mutect/HaplotypeCaller
### Description
**(Background)**
I've spent a lot of time working with Mutect2 in the past year (I've built a who…
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Hi,
I used csq on a big dataset and in general it is working great. But there are some cases were I am confused by the FORMAT/BCSQ field.
Here is one example:
13 102732665 13_1027326…
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https://arax.ncats.io/?source=ARS&id=df3f226a-571a-4219-ba5e-a37b7040ee18
No predicates or categories, CURIE on subject
![image](https://user-images.githubusercontent.com/83781286/125841734-3567…
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I am calling variants on _C. albicans_ strains genomes using the following workflow:
Read correction with Canu (v2.0)
Minimap2 for mapping reads against the reference (v2.17)
**Variant calling (m…
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Hello,
We are working on a dikaryotic (presence of two haploid nuclei coexist in one cell) fungal species, which is difficult to apply HiC scaffolding because it usually will brings two haplotypes to…
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I'm trying to perform ploidy aware variant calling with v2.17.2.
My cnv-map file is according to the specifications:
```
seq_name start end sample_name copy_number
34 100 200 sample1 9
34 500 6…
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Hi Xiaowen,
**I am wondering if it is possible to obtain a list of reads that contribute to each contig in the assembly?**
This seems like it would be highly valuable for metagenomics, as it can …
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Hi there,
I am running WhatsHap 1.0 using the following command:
``` whatshap phase --full-genotyping --include-homozygous --distrust-genotypes --mapq 1 --chromosome ${CHR} -r ${REF} -o ${OUT_VCF}…
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Dear Arne,
I'm having some trouble getting dentist to run on our university cluster with the example dataset. I haven't used snakemake before, so please excuse if I missed something very basic. Her…
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Hello,
Firstly, thanks for a very useful tool for somatic variant simulation.
As part of our simulation work we are using bamsurgeon (version 1.2) to try to create a virtual tumour BAM containin…