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friendsofstrandseq / mosaicatcher-pipeline

Integrated workflow for SV calling from single-cell Strand-seq data
https://friendsofstrandseq.github.io/mosaicatcher-docs/
MIT License
21 stars 10 forks source link

samtools version change #3

Closed maryamghr closed 2 years ago

maryamghr commented 4 years ago

samtools 1.10 has a bug in merging. It should be downgraded in the conda environment.

tobiasmarschall commented 4 years ago

There seem to be different flavors of 1.10: 1.10-3, 1.10-2, 1.10-1, 1.10-0... Does the bug apply to all of these? What exactly is that bug? Has it been reported to the samtools/htslib folks?

daewoooo commented 4 years ago

You can eventually use sambamba tools to do merging. Should even faster than samtools.

On Wed, Sep 16, 2020 at 1:55 AM Tobias Marschall notifications@github.com wrote:

There seem to be different flavors of 1.10: 1.10-3, 1.10-2, 1.10-1, 1.10-0... Does the bug apply to all of these? What exactly is that bug? Has it been reported to the samtools/htslib folks?

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