--callregions bed file requirements

[RichardCorbett]

Hi folks,

I am using 2.9.10 and found that when I provide a bed file to --callregions in the somatic workflow I need to be careful to format it appropriately.

Unbeknownst to me (by perhaps knownst to someone :) ) my initial run had a couple of bed entries that completely overlapped and possibly some entries that were out of order. When using that bed file the workflow ran in under 30 seconds and produced VCF files that contained only the header.

When I merge and sort the bed file I get successful results (ie. variants are called and limited to the regions listed in the bed file).

It appears that Strelka requires a well formatted bed file (sorted and merged?), but it didn't throw any errors (that I could find) when it was having a problem with my initial bed file.

Is it possible to throw an error when there is a problem with the bed file?

thanks Richard