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Problems with --callRegions

Open anfimoagbr opened this issue 5 years ago • 1 comments

Hi,

I'm trying to run Manta 1.6.0 on Centos 7, on targeted NGS data. I used the --callRegions and --exome options to use a BED file. However, I think the regions on the BED file are not being selected. Everytime I try to run Manta, I got this error: "CONFIGURATION ERROR: Reference genome mismatch: The length of chromosome 'chr1' is 249250621 in the reference fasta file but 249240622 in the Normal BAM/CRAM file. Strangely, my BED file starts on chr 2.

Is there something I need to change on the input file? Thanks,

anfimoagbr avatar Jun 26 '20 13:06 anfimoagbr

I also have this problem. Do you find the solutions?

YUYING07 avatar Oct 13 '22 05:10 YUYING07