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## Feature request
### Tool(s) or class(es) involved
Mutect/HaplotypeCaller
### Description
**(Background)**
I've spent a lot of time working with Mutect2 in the past year (I've built a who…
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I have four phased variants in close proximity that have the following pattern:
```
chrA 10 ... GT:PS 0|1:1
chrA 20 ... GT:PS 0|1:2
chrA 30 ... GT:PS 0|1:1
chrA 40 ... GT:PS 0|1:2
```
These…
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Hi,
I seem to have a similar issue to the one reported [here](https://github.com/swarris/Pacasus/issues/17). I am running on a server with Intel CPUs with Ubuntu 20.04.1.
This is the content of the …
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First thank you for writing a gpu aligner that actually offers appreciable benefits. (Even without nvlink).
I have been checking how the alignments compare to bwa2 alignments and noticed the followin…
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I find that I cannot type: `test-post` to jump to a directory called `test-box-postfix`, I have to type `postfix` to be able to jump in, but considering that I don't have any other directories contain…
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Hello,
I am trying to build Ugene from source, because I want it to work with Cuda.
The error is as follows.
>src/SWAlgorithmTask.cpp:23:26: fatal error: cuda_runtime.h: No such file or directory…
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Hello! First of all, I've said it before and I can't help but say it again: thank you for the great piece of software!
We all know that fzf is amazingly fast already. However, maybe there is still sp…
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If yes, is there any introduction, or any benchmark?
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I have a good quality GG/TC MNP:
```
$ freebayes -f /data/reference/ucsc/hg19/hg19.fa -r chr22:42526560..42526563 -F 0.3 reads.bam 2> /dev/null| cut -f1-6 | grep -v "##"
chr22 42526561 . GG …
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How do the scores in the align_local output relate to the #### marks in the a_edits list text?