<p>No, it's a bwa mem wrapper for bisulfite data essentially and bwa mem accepts fastq only.</p>

CC BY-SA 4.0
2023-04-23T00:44:21.890Z
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.
user172818
CC BY-SA 4.0
2023-04-21T08:56:48.417Z
2023-04-21T08:56:48.417Z
ATpoint
<p>Does <a href="https://github.com/brentp/bwa-meth" rel="nofollow noreferrer">bwameth</a> accept <code>bam</code> (unaligned) type as input or I will have to convert unaligned bam to fastq (<code>samtools fastq bam</code>) to use it as input?</p>

<sam><bwa><methylation>
Can bwameth accept unaligned Bam?
# Can bwameth accept unaligned Bam?

(Asked by: username_0 on 2023-04-19)

Does [bwameth](https://github.com/brentp/bwa-meth) accept `bam` (unaligned) type as input or I will have to convert unaligned bam to fastq (`samtools fastq bam`) to use it as input?

**Tags:** sam, bwa, methylation

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## 1 answers

### Answer by username_1 on 2023-04-21. Score: 2 | Accepted answer

No, it's a bwa mem wrapper for bisulfite data essentially and bwa mem accepts fastq only.

> **Comments:**
> **username_2**: 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.  

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