Hi,
I'm posting this here as I ran into trouble trying to run strelka on human data aligned to hs38DH - the reference built by bwakit to align to human build 38 plus decoys plus alternative sequences. The reference sequence has many HLA derived sequences that contain colons in the name, e.g. "HLA-A*01:01:01:01".
Initially I got the following error message:
BAM headers and reference fasta disagree on chromosome: HLA-A*01
To get things working I made two small changes to the configureStrelkaWorkflow.pl script. Firstly I modified line 281 from:
my @vals = split(':');
to
my @vals = split(':', $_, 2);
Secondly I added a one-liner at around line 354:
@chroms = grep(!/[\*\:]/, @chroms)
This causes strelka not to make calls on any chromosomes with colons or asterisks in the names, which is fine for my purposes and is a lot easier than trying to make everything work on those reference sequences.
With those two changes I could make it through configuration and got a Makefile that works.
Cheers,
-Tim Fennell