[BUG] ControlFreec issues with targeted sequencing data

[apeltzer]

Description of the bug

Running Sarek with -r dev and using a capture / targeted BED runs into trouble with ControlFreec.

https://github.com/BoevaLab/FREEC/issues/106 for more context, @FriederikeHanssen knows about it ;-)

Expected behaviour

ControlFreec just running through

Log files

Error: chromosome HLA-DRB1*16:02:01 present in your /foo/bar/baz/Homo_sapiens_assembly38.fasta.fai file was not detected in your file with capture regions wgs_calling_regions.hg38.bed
  Please solve this issue and rerun Control-FREEC

@chernomor reported it to me at BI, now reporting here so that @FriederikeHanssen has an issue

[FriederikeHanssen]

Thank you! I'll try to think of a temporary work around

[FriederikeHanssen]

I have added a patchy workaround in #728 . It will be part of release 3.0.2, hopefully by the end of the week. A length file containing only the relevant regions can be supplied with --cf_chrom_len .

I would close this issue, since I still have the one open in the controlfreec repository to hopefully get notified if anything changes upstream.

Let me know, if you run into any more issues regarding this!