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See this paper: http://www.nature.com/nbt/journal/v31/n3/abs/nbt.2514.html
(and the supplementary information) for details.
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I have managed to generate a minimal bam file that reproduces the issue.
First of all, you have to download the mini input.bam file from this dropbox link: https://www.dropbox.com/sh/xae79hanumpire…
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## Bug Report
### Affected tool(s) or class(es)
- Mutect2
### Affected version(s)
- Version:4.1.4.0 bioconda
### Description
vcf is produce but not .stat
#### Steps to reproduce
…
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Hi,
I'm having a problem with CNVRadar:
_**[2020-11-20 13:15:20] - main - INFO - User: lom
[2020-11-20 13:15:20] - main - INFO - Running from: cluster_calcul_cjp
[2020-11-20 13:15:20] - main - …
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| Name | Description | Size | Format | URL |
| --- | --- | --- | --- | --- |
| World Bank - Light Every Night | Light Every Night - World Bank Nightime Light Data – provides open access to all night…
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Hello,
The input vcf for PureCN should contain both germline and somatic variants. Does this mean both the germline and somatic vcf from variant caller should be combined together into a single one…
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The following one-liner (which I Googled, so I cannot vouch that this is the best way to do things) revealed 245Mb of files that are unused in master:
for ff in `find src/test/resources -name "…
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Happy to look into this, but it would be good if muTect supported running in tumour only mode or alternatively taking a vcf file instead of BAM for the normal(s).
For the first case it's sufficient …