Answers.Body: <p>No, it's a bwa mem wrapper for bisulfite data essentially and bwa mem accepts fastq only.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-04-23T00:44:21.890Z
Answers.Text: 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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Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-04-21T08:56:48.417Z
Answers.LastActivityDate: 2023-04-21T08:56:48.417Z
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Body: <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>
  
Tags: <sam><bwa><methylation>
Title: Can bwameth accept unaligned Bam?
ThreadText: # 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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