[DOCKTESTERS] BWA-Mem validation of DO51057 normal) 0.013% miss-matches, and 3.7% soft-matches, tumor) 0.043% miss-matches, and 4.64% soft-matches

[Miguel Vazquez]

Hi Christina,

There are two issues:

1- Splitting the BAM files and running them in the right order. Can do
2- That the order of the reads *inside* a BAM is the same. Can not fix

So if we would like the inquisitive user to reproduce the alignment process
from the available aligned BAM we need to tell him that the *reads* are not
in the same order and that about 3% of the reads will be aligned
differently.

Compared to the problem of the read order, the problem with the BAM
splitting and ordering is negligible, in fact, splitting the BAM i believe
did nothing at all to our numbers, so we might as well not even bother I
think, but there are people better suited than me to make this call.

In short, we can claim:

1) that the process is reproducible to a 99.99 percent using the original
unaligned BAM files
2) that working back from the aligned BAM one is able to reproduce the
results to a 96% accuracy, the lack on accuracy apparently due to different
read ordering.

The process to reproduce in 2) could be the simple one, just unalign the
BAM, or the more elaborate one that involves splitting the BAM an feeding
it in the right order, which does not seem to improve anything.
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