text: user5176: when mapping short reads with bwa mem, if a read has alternative mapping positions they are reported by bwa mem in the X0 and XA tags. 
  Now, let's say I want to compute the coverage of my bam file. How would I do for the alternative hits to be taken into accounts. What I mean is that, if a read QUERY has a selected best HIT position and 3 alternate HIT positions, I would like that QUERY read to be counted as 1 unit of coverage for the best HIT position, but also as 1 unit of coverage for each of the alternate HIT position. 
  My understanding is that samtools depth will only consider the best hit (which makes sense in 99.99% of the cases). 
  I guess I could edit the bam file with custom scripts so that the alternative hits are also reported as primary hits but I was wondering if there was an already existing tool (as I am not that confident with my ability to mess around with sam files). 
  Thanks a lot.
  
  user77: You would want to instead use the -a option with bwa mem to output all alignments. You would be best off filtering these with a custom script to only keep those with a close enough score to the primary hit. samtools depth can't be told to include secondary alignments (it's hard-coded), so you'll need to use something else like bamCoverage or samtools mpileup.
  
original_text: 5176: <p>when mapping short reads with bwa mem, if a read has alternative mapping positions they are reported by bwa mem in the X0 and XA tags. 
  Now, let's say I want to compute the coverage of my bam file. How would I do for the alternative hits to be taken into accounts. What I mean is that, if a read QUERY has a selected best HIT position and 3 alternate HIT positions, I would like that QUERY read to be counted as 1 unit of coverage for the best HIT position, but also as 1 unit of coverage for each of the alternate HIT position. </p>
  
  <p>My understanding is that samtools depth will only consider the best hit (which makes sense in 99.99% of the cases). </p>
  
  <p>I guess I could edit the bam file with custom scripts so that the alternative hits are also reported as primary hits but I was wondering if there was an already existing tool (as I am not that confident with my ability to mess around with sam files). </p>
  
  <p>Thanks a lot.</p>
   77: <p>You would want to instead use the <code>-a</code> option with <code>bwa mem</code> to output all alignments. You would be best off filtering these with a custom script to only keep those with a close enough score to the primary hit. <code>samtools depth</code> can't be told to include secondary alignments (<a href="https://github.com/samtools/samtools/blob/ffdddb6927827d805c603993cbc07a6faa9a63a6/bam2depth.c#L65" rel="nofollow noreferrer">it's hard-coded</a>), so you'll need to use something else like <code>bamCoverage</code> or <code>samtools mpileup</code>.</p>
  