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Hi @aryarm ,
I am running your pipeline starting with called peaks and a .BAM file. However, when doing a dry-run, I get the following error:
> "Building DAG of jobs...
> WorkflowError in line …
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- [x] try calling with Varscan
-> only calls the insertion but not the deletion....
- [x] dragen + evidence BAM
-> not conclusive, only part of the region covered in evidence BAM. Seems to su…
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Currently I am using following command to call variants using samtools/bcftools.
`samtools mpileup -d 1000000 -L 1000000 -uf ref.fasta sample.sorted.bam | bcftools view -vcg - > sample.SAMtools.vc…
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**Snakemake version**
### `Snakemake`
> 5.23.0
### Wrapper
**Issue**
I'm trying to adapt my regular VEP code to use the snakemake wrapper instead but am running into an issue.
I …
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Varscan 2.4.2 somatic VCF indel output file uses dashes in the Alt field, which should never appear as they are considered invalid characters in that field. For example, a single deletion might show …
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I am sorry, if I am asking too simple question but after reading read-me file, I am bit confused by the term unpaired data because I am using pair-end data in fastq file and finally after completion o…
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when I use `bcftools merge -l vcf.txt ">" merge.vcf` which vcf.txt contain /path/to/vcf what I want to merge . I found a BUG
for example:
> chr1 2595306 . C . . PASS A…
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Sorry,
I have some .bam files from WGS their average size is 70000000 KB. I tried Varscanbut I noticed even with 16 cpu calling mutations never finished finally after 36 hours session being killed …
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This is somewhat a matter of taste, but most (if not all) of the current modloadmsg usage seems like it would be better to have in the module "help" message instead, or deleted entirely. Having modul…
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I run the ~last~ latest version of vcf2maf on my data. I want to obtain ~vcf~ VAF comparable to data from TCGA.
I could not find VAF in the maf file of variants from tumor and normal
`"vcf2maf.pl --…