Does bwameth accept bam (unaligned) type as input or I will have to convert unaligned bam to fastq (samtools fastq bam) to use it as input?
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No, it's a bwa mem wrapper for bisulfite data essentially and bwa mem accepts fastq only.
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1$\begingroup$ You can pipe uBAM to bwamem with
samtools fastq in.bam | bwa mem -p - > out.sam, provided that paired-end reads are grouped by name. $\endgroup$ Commented Apr 23, 2023 at 0:44