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I'm using the example data from the documentation.
In v1.6.0 - the file `chr20.germline.vcf` does not get generated from the germline calling step.
```
${path}/src/Monopogen.py germline -a ${pa…
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Greetings,
I have a germline deletion candidate in a tumor/normal experiment that looks like the following going into 'varlociraptor preprocess variants'
`X 115190645 . GGGGG…
bwubb updated
1 month ago
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When I run prepocess.py with a sorted bam file, the following error occurs after some time: ValueError: fetch called on a bam file without index. How do I fix it?
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## Documentation request
I am trying to follow the germline joint variant best practices and am confused by the steps/examples and how it would work using real WGS or WXS data in a parallelized setti…
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For normal-tumor sample pair, when I run with somatic mode, I got a somatic variant in which normal variant allele frequency was 0.0526.
1 241680511 . T TA . PA…
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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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HaplotypeCaller
Call germline SNPs and indels via local re-assembly of haplotypes
Overview
The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplot…
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### Description of the bug
I was running Sarek for about 100 samples, and I ran out of disk quota at some point. After free up more space on the cluster (Uppmax), I `-resume` the previous run, but I …
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We usually filter variants against a panel of normal samples. This can be done post variant calling by genotyping detected variants in this panel and call anything at a certain threshold in a minimum …
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Dear Delly team,
Good evening.
In the output vcf file,
Alt showed without the insertion sequen…