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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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Methylcaller alternatives to recommended MethylDackel #67

Open Blosberg opened 3 years ago

Blosberg commented 3 years ago

Thanks very much for providing bwa-meth to the community.

The README recommends using MethylDackel for methylation calling/tabulation, etc., however MethylDackel has had a critical error leading to a seg-fault/core-dump which, apparently, has been unresolved for a few months now. In looking for alternatives, I tried using mcall, but mcall log shows the following error:

[..]
XR:Z or ZR:Z:, or ZS:Z: field not found
[..]

I know this isn't really your responsibility, but can you recommend an alternative methyl-caller package to use downstream of bwameth until the issue with MethylDackel is resolved? thanks for any advice you can offer.

brentp commented 3 years ago

It looks like a solution there is to build with htslib 1.9 instead of relying on the conda build. (You could also try htslib 1.11 which is released today). I don't know of other tools beyond MethylDackel.