text: user1194: Is there a way to filter bases in BAM files based on phred quallities through python's pysam ?
  I have a code here that
  
  Takes the nucleobases per position from a BAM file using pysam's pileup function
  Saves it in ReverseList and ForwardList based on both strands (i.e forward and reverse), I want to reject those bases that have phred quality below 25 to be not stored in the ForwardList and ReverseList lists so that they are not used for further analysis.
   samfile = pysam.Samfile( filename, "rb" )
   ReverseList = [''] * lenref
   ForwardList = [''] * lenref
   for pileupcolumn in samfile.pileup() :
       for pileupread in pileupcolumn.pileups:
           if (pileupread.alignment.mapping_quality <= 15):
                 continue      
           if not pileupread.is_del and not pileupread.is_refskip:
                 if pileupread.alignment.is_reverse: #negative
                        ReverseList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
                 else:
                        ForwardList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
  
   samfile.close()
  
  
  Where lenref = 16569(length of mitochondrial genome) and filename is the name of BAM file. I want to filter based of phred qualities of bases.
  
  user77: The PileupRead object as a query_position attribute, which you can use for this:
  for pileupcolumn in samfile.pileup() :
      for pileupread in pileupcolumn.pileups:
           if (pileupread.alignment.mapping_quality <= 15):
               continue      
           if not pileupread.is_del and not pileupread.is_refskip:
               if pileupread.alignment.query_qualities[pileupread.query_position] < 10:
                   # Skip entries with base phred scores < 10
                   continue
               if pileupread.alignment.is_reverse: #negative
                     ReverseList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
               else:
                     ForwardList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
  
  Note the 6th line, which implements a filter with a threshold of 10.
  
original_text: 1194: <p>Is there a way to filter bases in BAM files based on phred quallities through python's pysam ?</p>
  
  <p>I have a code here that</p>
  
  <ul>
  <li>Takes the nucleobases per position from a BAM file using pysam's pileup function</li>
  <li><p>Saves it in ReverseList and ForwardList based on both strands (i.e forward and reverse), I want to reject those bases that have phred quality below 25 to be not stored in the ForwardList and ReverseList lists so that they are not used for further analysis.</p>
  
  <pre><code> samfile = pysam.Samfile( filename, "rb" )
   ReverseList = [''] * lenref
   ForwardList = [''] * lenref
   for pileupcolumn in samfile.pileup() :
       for pileupread in pileupcolumn.pileups:
           if (pileupread.alignment.mapping_quality &lt;= 15):
                 continue      
           if not pileupread.is_del and not pileupread.is_refskip:
                 if pileupread.alignment.is_reverse: #negative
                        ReverseList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
                 else:
                        ForwardList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
  
   samfile.close()
  </code></pre></li>
  </ul>
  
  <p>Where lenref = 16569(length of mitochondrial genome) and filename is the name of BAM file. I want to filter based of phred qualities of bases.</p>
   77: <p>The PileupRead object as a query_position attribute, which you can use for this:</p>
  
  <pre class="lang-py prettyprint-override"><code>for pileupcolumn in samfile.pileup() :
      for pileupread in pileupcolumn.pileups:
           if (pileupread.alignment.mapping_quality &lt;= 15):
               continue      
           if not pileupread.is_del and not pileupread.is_refskip:
               if pileupread.alignment.query_qualities[pileupread.query_position] &lt; 10:
                   # Skip entries with base phred scores &lt; 10
                   continue
               if pileupread.alignment.is_reverse: #negative
                     ReverseList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
               else:
                     ForwardList[pileupcolumn.pos] += pileupread.alignment.query_sequence[pileupread.query_position]
  </code></pre>
  
  <p>Note the 6th line, which implements a filter with a threshold of 10.</p>
  