format_reads for bwa-meth's SAM files

smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

http://smithlabresearch.org/methpipe

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format_reads for bwa-meth's SAM files #215

Closed diegommcc closed 1 year ago

diegommcc commented 2 years ago

Hello,

I'm working on a methyl ATAC-seq data generated using the experimental protocols described here. I've used bwa-meth to align the reads, but I've realized that methpipe now uses format_reads to merge paired-end mates into single-end entries. However, bwa-meth is not supported. I was wondering if there is any way to format bwa-meth BAM files in order to generate valid SAM files for methpipe.

Thanks in advance.

andrewdavidsmith commented 1 year ago

@diegommcc sorry for the slow (or non) response. I don't think it's realistic at this time. Please comment again if you plan to keep using bwa-meth in the future. If enough people request this then it might be possible.