title: BAM file is incorrectly aligned
body: <p><a href="https://i.stack.imgur.com/xy1J9.png" rel="nofollow noreferrer">image of igv showing shifted bam file alignment</a></p>
  <p>I ultimately want to use scRNAseq data (BD Rhapsody) to call variants in the mtDNA sequence.</p>
  <p>I've run my data through sevenbridges (BD Rhapsody™ WTA Analysis Pipeline (Revision 6)).</p>
  <p>I input my reference genome including mitochondrial sequence.</p>
  <p>I have an outputted BAM file which I want to run mpileup on to find variants.</p>
  <p>However, when I open my BAM file in IGV, I notice the BAM file is not well aligned to my reference sequence.</p>
  <p>In some places it is &quot;x&quot; number of shifted bases misaligned. For example in the image you can see the alignment should be 1 base back.</p>
  <p>This seems odd to me. If the sequence alignment was 1 base back surely the software would consider that a better alignement. It's also strange that the reads are a set number out, rather than just randomly dispersed. Has anyone else ever seen a BAM file have shifted alignment?</p>
  <p>Alan</p>