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Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
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Problems with --callRegions #231

Open anfimoagbr opened 4 years ago

anfimoagbr commented 4 years ago

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,

YUYING07 commented 1 year ago

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