<p>You're looking for <code>pileup</code>, which is the htslib (and thus samtools/bcftools) method for finding variants. See <a href="https://pysam.readthedocs.io/en/latest/api.html#introduction" rel="nofollow noreferrer">this section</a> of the pysam documentation. You may want to peruse about <a href="https://pysam.readthedocs.io/en/latest/api.html#pysam.PileupColumn" rel="nofollow noreferrer">the output</a> as well. The gist is:</p>
<pre><code>import pysam
samfile = pysam.AlignmentFile(&quot;ex1.bam&quot;, &quot;rb&quot; )
for pileupcolumn in samfile.pileup(&quot;chr1&quot;, 100, 120):
    for pileupread in pileupcolumn.pileups:
        if not pileupread.is_del and not pileupread.is_refskip:
            # query position is None if is_del or is_refskip is set.
            ...handle mismatches...
</code></pre>

CC BY-SA 4.0
2020-12-16T16:12:57.067Z
Thanks for the response! I think this would work but it's less than ideal since I would be iterating over each read multiple times, no? I'm wondering if it's possible to iterate over the list of reads that span a region and retrieve that same information without going over pileup columns.
juniper-
CC BY-SA 4.0
2020-12-16T16:17:06.587Z
Also, this bit of code `for pileupread in pileupcolumn.pileups` crashes the Python kernel when running inside of an IPython notebook :-/
juniper-
CC BY-SA 4.0
2020-12-16T07:49:43.570Z
2020-12-16T07:49:43.570Z
Devon Ryan
<p>Ideally, I'd like to do something like the following:</p>
<pre><code>f = pysam.AlignmentFile(filename, index_filename=index_filename)
read = list(f.fetch('Chromosome', 1, 10000))[0]
read.get_variations()
</code></pre>
<p>And have that output something like:</p>
<pre><code>[
  (1, 'A', 'C'), # An A -&gt; C mismatch at position 1
  (15, 'I', 'CGGG'), # An insertion of the string 'CGGG' starting at position 15 of the read
  (32, 'D', 4), # A deletion of 4 base pairs starting at position 32
]
</code></pre>
<p>I know that it's possible to figure out all of those values by parsing the CIGAR string and MD tags but I'm wondering if there's a more intuitive interface.</p>

<sam>
Is there a straightforward way to get mismatches/indels in a BAM file using pysam?
# Is there a straightforward way to get mismatches/indels in a BAM file using pysam?

(Asked by: username_0 on 2020-12-16)

Ideally, I'd like to do something like the following:
f = pysam.AlignmentFile(filename, index_filename=index_filename)
read = list(f.fetch('Chromosome', 1, 10000))[0]
read.get_variations()

And have that output something like:
[
  (1, 'A', 'C'), # An A -> C mismatch at position 1
  (15, 'I', 'CGGG'), # An insertion of the string 'CGGG' starting at position 15 of the read
  (32, 'D', 4), # A deletion of 4 base pairs starting at position 32
]

I know that it's possible to figure out all of those values by parsing the CIGAR string and MD tags but I'm wondering if there's a more intuitive interface.

**Tags:** sam

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## 1 answers

### Answer by username_1 on 2020-12-16. Score: 1

You're looking for pileup, which is the htslib (and thus samtools/bcftools) method for finding variants. See this section of the pysam documentation. You may want to peruse about the output as well. The gist is:
import pysam
samfile = pysam.AlignmentFile("ex1.bam", "rb" )
for pileupcolumn in samfile.pileup("chr1", 100, 120):
    for pileupread in pileupcolumn.pileups:
        if not pileupread.is_del and not pileupread.is_refskip:
            # query position is None if is_del or is_refskip is set.
            ...handle mismatches...

> **Comments:**
> **username_0**: Thanks for the response! I think this would work but it's less than ideal since I would be iterating over each read multiple times, no? I'm wondering if it's possible to iterate over the list of reads that span a region and retrieve that same information without going over pileup columns.  
> **username_0**: Also, this bit of code `for pileupread in pileupcolumn.pileups` crashes the Python kernel when running inside of an IPython notebook :-/  

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