I am getting stuck in the MergeBamAlignment step of the Mitochondrial short variant discovery best practices workflow. In fact, I am working with the build37.2 reference and to run MergeBamAlignment as described on the workflow, I have prepared the following files :
ALIGNED: bam file including exclusively all reads aligned to MT chromosome generated as a subset from whole exome bam file using PrintReads.
UNMAPPED: bam generated by RevertSam on the previous step bam file
Now as a reference file, I was aiming to use a shifted MT chromosome fasta file so I wonder if I am right and if so, it happens that I didn't find my path to create this shifted file knowing that ShiftFasta didn't work for me.
Please, is there any instructions to create shifted mitochondrial reference file or recommendations about best practices regarding the use of the MergeBamAlignment with regards to mitochondrial variant discovery.
Ahmed S. Chakroun
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