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hi all,
I am trying to annotate a project .vcf file retrieved from GLnexus with OpenCRAVAT.
the .bcf file file gets converted to an .vcf file with:
`bcftools view | bgzip -c > pvcf_all_glnexus.…
loipf updated
3 years ago
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@Moult I should've made an issue here instead of posting in chat 😂
https://github.com/IfcOpenShell/IfcOpenShell/blob/364138d40818268b2e1bede8412d038e35e2684a/src/blenderbim/blenderbim/bim/module/b…
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## Bug Report
### Affected tool(s) or class(es)
gatk GenotypeGVCFs
### Affected version(s)
- [X] Latest public release version [GATK 4.1.9.0]
- [ ] Latest master branch as of [date of test?]
…
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### Describe the bug
I consider this as bug, not having control over content.
Padding is forced to be 12,0,0,0. Why fixed?
Alignment is set to center. Why fixed.
### To Reproduce
```
…
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Hey Mike
I downloaded BamM today and tried to install it on CentOS6.6 (with python2.7, python2.7 numpy, samtools and bwa tools):
```
$ git clone https://github.com/minillinim/BamM.git
$ cd BamM
$ p…
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Hi,
I have sequenced a single gene using naopore minion sequencer, aligned the reference genome, and I now want to call variants. I have some SNP genotypes for my target gene which I am going to us…
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Thanks for all of your work on TBProfiler. Running;
```
tb-profiler profile --bam rpoB.bam --external_db tbdb/tbdb
```
This worked on v5, but now on v6.2.1 (installed from conda) getting the bel…
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Hi,
Is there a way to configure this permanently within the bcftools path, for example in a config file? As opposed to defining this environment variable each time.
Or making a default search path…
gevro updated
3 weeks ago
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I cannot install somehow cyvcf2. I upgraded to python 3.9.x and also updated visual studio.
```
Running setup.py install for cyvcf2 ... error
error: subprocess-exited-with-error
× Running …
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Trying to run minimac4 v4.1.2 I am getting segmentation faults:
minimac v4.1.2
Imputing 1:1-20000000 ...
Loading target haplotypes ...
Loading target haplotypes took 0 seconds
Loading reference…