Excluded regions

[bounlu]

I am using delly call with a BAM file with a reference fasta file different than originally used for the alignment. So the chromosomes are not compatible causing the below error:

delly call \
	-g genome.fa \
	-x human.hg38.excl.tsv \
	-o x.vcf \
	x1.deduplicated.sorted.bam \
	x2.deduplicated.sorted.bam

BAM file chromosome chr1_KI270762v1_alt is NOT present in your reference file genome.fa

However, I would expect this shouldn't be a problem since that chromosome is already in the excluded regions file:

$ grep chr1_KI270762v1_alt human.hg38.excl.tsv 
chr1_KI270762v1_alt

How to fix this in the best way?

[tobiasrausch]

Alignments and delly have to use the same reference genome. This caused many problems in the past and that's why delly is very strict and requires the same reference genome.