Reference genome mismatch

[rmurphy49]

Running the following command line for the configuration of Manta led to the following configuration error:

configManta.py --normalBam /mnt/scratch/users/40057929/MCL*/MCL*/12-2164*/12-2164-01_MRDneg_S1.bam --tumorBam /mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309*/04-0309-01_S2.bam --referenceFasta /mnt/scratch/users/40057929/BWA/hg38bwaidx.fa --runDir /users/40057929/

CONFIGURATION ERROR:
Reference genome mismatch: Reference fasta file is missing a chromosome found in the Normal BAM/CRAM file: 'chr1'

This is despite the fact the reference genome does have chromosome 1. It may be important to note that the reference genome is not exactly the same as the reference genome used to create the BAM files. Any advice or help?

[ctsa]

The reference fasta needs to match the input alignment files. Is it possible your fasta contains a chromosome 1 using a different label (eg. "1")?

[rmurphy49]

I obtained the same reference fasta that was used for the initial alignment which fixed the problem. Thanks for the quick reply and help!