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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
139 stars 53 forks source link

SNP Question #43

Closed tantrev closed 7 years ago

tantrev commented 7 years ago

Just wondering if the bam file generated by bwa-meth file can be used directly in other SNP callers like biscuit? My (naive) self is just curious since bwa-meth performs the C -> T conversion to speed up alignment.

brentp commented 7 years ago

Yes, the should be usable. It converts C->T for alignment, but then writes out the original read.

tantrev commented 7 years ago

Perfect, thank you!

tantrev commented 7 years ago

On a related note, do you by chance have any thoughts on the proper way to extract discordant and split reads from WGBS data? I've been trying different methods and have gotten drastically different results, as outlined in this lumpy ticket.

brentp commented 7 years ago

the discordant flag isn't reliable from bwa meth (and therefore the flag isn't useful). It updates what it thinks is discordant within each processing chunk. So best to use lumpy_filter or something other than the flag.

tantrev commented 7 years ago

@brentp - thank you! I'm not quite sure how to invoke the lumpy_filter, but I'll try posting in that lumpy ticket to see if anybody has any ideas.