Answers.Body: <p>There's an example in the README (<a href="https://github.com/epifluidlab/cragr#example-datasets" rel="nofollow noreferrer">https://github.com/epifluidlab/cragr#example-datasets</a>):</p>
  <blockquote>
  <p>For you information, below are steps from the BAM file to the
  fragment file:</p>
  </blockquote>
  <pre class="lang-none prettyprint-override"><code>samtools sort -n -o qsorted.bam -@ 4 sample.bam
  samtools view -h -f 3 -F 3852 -G 48 --incl-flags 48 qsorted.bam |\
    bamToBed -bedpe -mate1 -i stdin |\
    awk -F'\t' -v OFS=&quot;\t&quot; '{if ($1!=$4) next; if ($9==&quot;+&quot;) {s=$2;e=$6} else {s=$5;e=$3} if (e&gt;s) print $1,s,e,$7,$8,$9}' |\
    sort -k1,1V -k2,2n |\
    bgzip &gt; sample.frag.bed.gz
  tabix -p bed sample.frag.bed.gz
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-02T04:29:38.607Z
Answers.LastActivityDate: 2023-08-02T04:29:38.607Z
Answers.UserDisplayName: jared_mamrot
Body: <p>Im trying to follow this pipeline <a href="https://github.com/epifluidlab/cragr" rel="nofollow noreferrer">https://github.com/epifluidlab/cragr</a> on cfDNA WGS. I have bam files from paired end reads aligned with bwa mem.</p>
  <p>The workflow requires bgzipped and indexed fragment data files as input.
  <a href="https://i.sstatic.net/CJ4Gt.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/CJ4Gt.png" alt="enter image description here" /></a></p>
  <p>I have been searching how can I obtain BED files from fragments coordinates instead of reads coordinates, and came up with no answer.</p>
  <p>Does someone know how can I obtain such bed file?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-01T19:45:48.847Z
Comments.Text: Hi, what do you mean? :) I don't know how to do it. I'm familiar with bamtobed from bedtools but that gives me a bed file based on reads. I need a bed file based on fragments instead :)
Comments.UserDisplayName: Julieta
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-01T21:39:22.193Z
Comments.Text: I see so you are looking whether there is a bedtools option for fragment output. Got it, thanks. Would be good to modify the question with the info.
Comments.UserDisplayName: M__
Tags: <sam><bed><bedtools><wgs><epigenetics>
Title: obtaining a fragment data file bed from bam
ThreadText: # obtaining a fragment data file bed from bam
  
  (Asked by: username_0 on 2023-08-01)
  
  Im trying to follow this pipeline <https://github.com/epifluidlab/cragr> on cfDNA WGS. I have bam files from paired end reads aligned with bwa mem.
  
  The workflow requires bgzipped and indexed fragment data files as input.
  [![enter image description here](https://i.sstatic.net/CJ4Gt.png)](https://i.sstatic.net/CJ4Gt.png)
  
  I have been searching how can I obtain BED files from fragments coordinates instead of reads coordinates, and came up with no answer.
  
  Does someone know how can I obtain such bed file?
  
  **Tags:** sam, bed, bedtools, wgs, epigenetics
  
  > **Comments:**
  > **username_0**: Hi, what do you mean? :) I don't know how to do it. I'm familiar with bamtobed from bedtools but that gives me a bed file based on reads. I need a bed file based on fragments instead :)  
  > **username_1**: I see so you are looking whether there is a bedtools option for fragment output. Got it, thanks. Would be good to modify the question with the info.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-08-02. Score: 2
  
  There's an example in the README (<https://github.com/epifluidlab/cragr#example-datasets>):
  
  > For you information, below are steps from the BAM file to the
  > fragment file:
  
  ```none
  samtools sort -n -o qsorted.bam -@ 4 sample.bam
  samtools view -h -f 3 -F 3852 -G 48 --incl-flags 48 qsorted.bam |\
    bamToBed -bedpe -mate1 -i stdin |\
    awk -F'\t' -v OFS="\t" '{if ($1!=$4) next; if ($9=="+") {s=$2;e=$6} else {s=$5;e=$3} if (e>s) print $1,s,e,$7,$8,$9}' |\
    sort -k1,1V -k2,2n |\
    bgzip > sample.frag.bed.gz
  tabix -p bed sample.frag.bed.gz
  
  ```
  
  
  ---
  
  