strelka2 complaining about unknown chromosome, while I have removed that from bam

Question

[ruhollah]

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

Answer 1

[GenoMax]

Did you examine the BAM header to make sure the chromosomes were not listed there?

[ruhollah]

You got it! Extremely helpful hint! thank you! I checked the bam header and all of those unknown chrs are there.

The only way I can think to get rid of the unknown/random chr in the header, is to:

1. first convert bam files to sam (to make it text editable)
2. then remove those lines in the header of the sam file (using sed in-place: sed -i '/^\@SQ.*\_/d' my_sam_file.sam)
3. then convert back the sam to new bam

This is tedious though. do you have any suggestion?

Thank you so much!

[GenoMax]

Or try the method described in : C: How to change a BAM file so the chromosome identifier is "chr 1" not just "1" or How to change SM tag in bam file

[ruhollah]

I did not know about the samtools reheader. this was very helpful!

thank you so much!