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We create this type of report for researchers, this way they can see at a glance how the experiment worked:
sample | host | Virus sequence | total reads | reads host | % reads host | reads virus | …
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I'm trying to run vcf_santize.cwl as part of a germline variant detection process. As best I can tell, subworkflows/varscan_germline.cwl is calling fp_filter.cwl, which is calling vcf_sanitize.cwl
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**Version info**
- bcbio version (bcbio_nextgen.py --version): 1.2.3
- OS name and version: Ubuntu 19.10
**To Reproduce**
bcbio_nextgen.py upgrade -u development --tools --data
**Observed b…
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Hi !
I would like to ask, the data types downloaded by TCGA are different from the four types recommended by this software package `MuTect2, FreeBayes, VarDict and VarScan`. so can I use use 2 or 3 t…
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I've traced the error to vt normalize in this line of ggd-run.sh:
```
bcftools view -f PASS $vcf_file | bcftools annotate -x "^$fields_to_keep" -Ov | vt decompose -s - | vt normalize -r $ref -n - …
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Hi,
I can't seem to get NASP to process.
It can set up all the folders
ls
bwamem matrices matrix_dto.xml nasp_matrix.out reference results-config.xml runlog.txt samtools statistics trim…
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I have a number (18) of bam files with alignments from a total of 5 samples. I have added @RG lines to these with SM:sample_ids. When I run samtools mpileup with these samtools reports (correctly) 5 s…
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Hi,
I am testing SMuRF on a set of files I generated running the individual callers. I am getting an "Error in normalizeDoubleBracketSubscript". It seems that the expected data type is not there. A…
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**Describe the bug**
A clear and concise description of what the bug is.
`samtools sort` is failing on output of `ivar trim` with v1.2.1 of `iVar` on Bioconda. This wasnt an issue with v1.2. Appar…
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Hello
I tried to install SLAMdunk using your recommendation:
conda create --name myenv -c bioconda slamdunk
From some reasons, while runnig SLAMdunk I have error.
The log file message is:
.loc…