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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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I use snippy 4.6.0 to calling my bacteria snp,but there are no result ,I wonder what to do next ,thanks.
snippy --outdir 135080RSH2439 --ref 175001_wt/175001R1qc_shovill.fasta --ctgs 135080RSH2439.fa…
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Hi,
I used bwa-meth to align rust infected wheat samples to the rust genome. However, when I ran samtools flagstat I get the follow output:
```
22806328 + 4861610 in total (QC-passed reads + QC…
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#### Is your feature request related to a problem? Please specify.
Yes. I am support staff and I need to help out a user. The user used `samtools quickcheck` to check her file to be correct. It was…
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I'm using genome-guided assembly like this:
_Trinity --no_version_check --genome_guided_bam Nona.sorted.bam --genome_guided_max_intron 10000 --max_memory 4G --CPU 8 --output trinity_Nona_guided_
A…
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If I'm not mistaken, the scritpt `run_ataqc.py` is broken due to a change of API in `samtools sort`, notably lines [522](https://github.com/kundajelab/ataqc/blob/d5b65453e25cc6481692cd46e8cfeae8a61850…
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Something seemed to have changed around Singularity v4 that prevents Singularity from pulling images that are too old:
```
$ singularity --version
singularity-ce version 4.0.3-jammy
$ singularity …
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Hi,
Thank you very much for writing MethylDackel. I'm running into a conflict of the libcurl version number on my setup.
When running MethylDackel, I get
```
MethylDackel: /usr/lib/x86_64-linux-g…
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Sambamba is faster at processing SAM/BAM files. In addition, we should provide a streaming example to show the benefits of piping the commands for one single execution to produce BAM.
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I've been using the biodalliance embedded genome browser, but it doesn't support CRAM formatted files, so I was thinking creating a minion web service to wrap a samtools conversion command. Has anyone…