text: user868: I have Illumina MiSeq paired-end reads from 150bp amplicons mapped to my reference genome (> 1000X coverage). These reads have indels that may or may not induce frameshifts. If the indel induces a frameshift (i.e. indel is not a multiple of 3bp), I want to know if that leads to a stop codon later in the read. Is there any package/method that would allow me to do this?
  Few extra details
  
  I might be wrong but I think this is different than gene prediction as I would want the tool to scan each read in the correct frame; not try different frames to detect ORFs etc.
  I expect mosaicism, so I do not want to compute a single assembly/consensus and predict stop codons in it.
  
  Here is how I imagine such a script/tool would work:
  
  Take the position of the first translated codon of the exon I am interested in (from Ensembl for instance?). Eg. gene abc/exon1 starts at chr1:1000.
  
  Then for each read:
  
  Look at which position the read is mapped to my reference. Eg. read 1 is mapped to chr1:1050.
  Compute the position of the first full codon in the correct frame in my read. Eg. start codon at chr1:1000 but my read starts at chr1:1050, the first full translated codon in my read should start at chr1:1052 (I think?).
  Split all my read into 3-mers starting at that position and build something like a 3-mer/position dictionnary. 
  Look for stop codons and report the positions.
  
  Does it exist?
  
  user2388: With 150bp reads, you might be able to blastx all the unique sequences you've got against the target proteins.
  
original_text: 868: <p>I have Illumina MiSeq paired-end reads from 150bp amplicons mapped to my reference genome (> 1000X coverage). These reads have indels that may or may not induce frameshifts. If the indel induces a frameshift (i.e. indel is not a multiple of 3bp), I want to know if that leads to a stop codon later in the read. Is there any package/method that would allow me to do this?</p>
  
  <p>Few extra details</p>
  
  <ul>
  <li>I might be wrong but I think this is different than gene prediction as I would want the tool to scan each read in the correct frame; not try different frames to detect ORFs etc.</li>
  <li>I expect mosaicism, so I do not want to compute a single assembly/consensus and predict stop codons in it.</li>
  </ul>
  
  <p>Here is how I imagine such a script/tool would work:</p>
  
  <ol>
  <li>Take the position of the first translated codon of the exon I am interested in (from Ensembl for instance?). <em>Eg. gene abc/exon1 starts at chr1:1000.</em></li>
  </ol>
  
  <p>Then for each read:</p>
  
  <ol start="2">
  <li>Look at which position the read is mapped to my reference. <em>Eg. read 1 is mapped to chr1:1050.</em></li>
  <li>Compute the position of the first full codon in the correct frame in my read. <em>Eg. start codon at chr1:1000 but my read starts at chr1:1050, the first full translated codon in my read should start at chr1:1052 (I think?).</em></li>
  <li>Split all my read into 3-mers starting at that position and build something like a 3-mer/position dictionnary. </li>
  <li>Look for stop codons and report the positions.</li>
  </ol>
  
  <p>Does it exist?</p>
   2388: <p>With 150bp reads, you might be able to blastx all the unique sequences you've got against the target proteins.</p>
  