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Hello MutSig2CV Authors,
In the instructions for param file it says that the example file is available in test/input/params.txt. but there is no test folder.
I made a params_file.txt file stati…
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Hi, thank you for the fantastic package!
I initially ran TRUST4 with an earlier version that I guess did not output in an airr format. I know you can convert the existing barcode report to this for…
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Hello,
I have run CPSR on some germline samples, and am looking at the biomarker section now. I see that class 4 and 5 variants overlapping the CIViC markers are considered, however, the biomarker…
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
params.data_dir = 'output/4.markDuplicate'
params.reference = 'reference/Homo_sapiens_assembly38.fasta'
params.bed_file = 'reference/hg38_exo…
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I get a `No snps found in normal!` error when I attempt to run Hatchet2 using `reference_version=hg38`. Reference fasta files are hg38. Interestingly, when I run the relevant `bcftools` commands from …
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Hi
I am trying to understand the output data for detecting somatic copy number alternations using WGS data.
I have two file (*_CNVs). One is the file, which is obtained from BAM file as input, and…
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Hi Team,
Am actually using the TCGA data to run on the guacamole. I am confused like where should I pass the human reference hg19 file to variant calling or genotyping. Something like we …
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Hello
This issue is related to the following: https://github.com/Illumina/manta/issues/93
I'm configuring Manta as follows (and the bug is the same for germline or TN pairs)
```
configManta…
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As in varscan's default txt output, there are more stats info including filtering for high confident variants, that would be helpful for mucor to support this input format like it supports mutect's tx…
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This is a marker for the issues we discussed on the AIRR-SW-WG call today.
Some characteristics of real-world data sets:
- Many data sets do not cover the entire V-region. It's quite common today…