Hi!

I hope all of you and your loved ones are doing well, while we are all working remotely during the covid era.

I am trying to find somatic mutations for WES in mm10 using strelka2 by the following command (as suggested in their github):

$configureStrelkaSomaticWorkflow.py --normalBam /Dir_to_normal_bam/My_final_normal.bam --tumorBam /Dir_to_tumor/My_final_tumor.bam --referenceFasta /Dir_to_mm10/mm10.fa --runDir demo_somatic  --exome

It keeps complaining with the following err:

CONFIGURATION ERROR:
Reference genome mismatch: Reference fasta file is missing a chromosome found in the normal BAM/CRAM file: 'chr1_GL456210_random'

Needless to say, I have already sorted, re-indexed, extracted only known chromosomes into new bam files, and indexed the new bam files using samtools for normal and tumor bam files, using the following snippet:

samtools sort my_normal_bam.bam  -o sorted_my_normal_bam.bam   &&  samtools index sorted_my_normal_bam.bam  &&  samtools view -o  My_final_normal.bam  sorted_my_normal_bam.bam    `seq 1 19 | sed 's/^/chr/'  &&  echo X | sed 's/^/chr/' && echo Y | sed 's/^/chr/'`

Any suggestion / comments would be highly appreciated