text: user8665: so I'm having a problem using samtools phase. 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!
  
  user7349: This is what I see in my samtools phase (v1.10)
  Usage:   samtools phase [options] <in.bam>
  
  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]
  
  
original_text: 8665: <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>
   7349: <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>
  