Parallelization for Haplotypecaller about exoseq

[marchoeppner]

Hi,
WGS will not be part of ExoSeq at this time as we decided that certain design elements (especially for maximum parallelization) would likely be different. The Sarek pipeline currently offers robust WGS calling, so ExoSeq will (likely) do what it says on the box, exomes.

However, we will look into speed improvements as suggested. We are currently passing the exome kit target as interval list to HC; I am not sure that splitting this file into chunks would really result in vast speed improvements (since the targets are usually pretty small anyway), but it is worth checking.

[ewels]

Sarek: https://github.com/SciLifeLab/Sarek

[apeltzer]

Speedups for Exome Capture Kits are negligible, so this is not worth the effort. To even gain speed, we'd need to merge intervals together in chunks to work on as otherwise the I/O required to query each interval eats up the benefits. Closing this therefore!