<p>This is what I see in my samtools phase (v1.10)</p>

<pre><code>Usage:   samtools phase [options] &lt;in.bam&gt;
</code></pre>

<p>samtools phase only takes a bam file as an input. But you are specifying a .fasta file as an input. If you want to specify the reference genome, you should be using the argument "--reference" as described here</p>

<pre><code>      --reference FILE
           Reference sequence FASTA FILE [null]
</code></pre>

CC BY-SA 4.0
2020-04-23T13:34:03.290Z
Oh, you're right! I also tried that but it didn't work. I managed to make it work and I'll add an answer shortly. But before that I want to ask a little question:  in my pipeline I also remove pcr duplicates with the fixmate/markdup steps. Is it better to phase the reads before or after removing the duplicates?
Wtwiki
CC BY-SA 4.0
2020-04-23T18:05:23.627Z
I would recommend removing duplicates first.
Geraldine_VdAuwera
CC BY-SA 4.0
2020-04-22T23:31:54.473Z
2020-04-22T23:31:54.473Z
KT8
<p>so I'm having a problem using <a href="http://www.htslib.org/doc/samtools-phase.html" rel="nofollow noreferrer">samtools phase</a>. I'm trying to phase my .bam archives that where generated by aligning my samples with my reference genome. Following the documentation I tried the command: </p>

<p><code>samtools phase -A  my_referenceGenome.fasta   my_sample_toBePhased.bam</code></p>

<p>The -A flag stands for dropping reads with ambiguous phase. The <strong>error</strong> I get is: <code>[W::sam_read1] Parse error at line 1</code>. I generated .bam files with and without the SAM header but the error persists.</p>

<p>I feel like I am missing something basic but that isn't clearly stated anywere. Does the <code>my_referenceGenome.fasta</code> archive needs to be previously phased? If so, how can I do it?</p>

<p>Thank you so much!</p>

<sam><fasta><samtools><phase>
Phasing problem using "samtools phase"
# Phasing problem using "samtools phase"

(Asked by: username_0 on 2020-04-22)

so I'm having a problem using [samtools phase](http://www.htslib.org/doc/samtools-phase.html). I'm trying to phase my .bam archives that where generated by aligning my samples with my reference genome. Following the documentation I tried the command:

`samtools phase -A my_referenceGenome.fasta my_sample_toBePhased.bam`

The -A flag stands for dropping reads with ambiguous phase. The **error** I get is: `[W::sam_read1] Parse error at line 1`. I generated .bam files with and without the SAM header but the error persists.

I feel like I am missing something basic but that isn't clearly stated anywere. Does the `my_referenceGenome.fasta` archive needs to be previously phased? If so, how can I do it?

Thank you so much!

**Tags:** sam, fasta, samtools, phase

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## 1 answers

### Answer by username_1 on 2020-04-22. Score: 2

This is what I see in my samtools phase (v1.10)
Usage:   samtools phase [options] 

samtools phase only takes a bam file as an input. But you are specifying a .fasta file as an input. If you want to specify the reference genome, you should be using the argument "--reference" as described here
      --reference FILE
           Reference sequence FASTA FILE [null]

> **Comments:**
> **username_0**: Oh, you're right! I also tried that but it didn't work. I managed to make it work and I'll add an answer shortly. But before that I want to ask a little question:  in my pipeline I also remove pcr duplicates with the fixmate/markdup steps. Is it better to phase the reads before or after removing the duplicates?  
> **username_2**: I would recommend removing duplicates first.  

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