Reference doesn't match the input's build in variant calling pipe line

Question

[langziv]

Hello.

The error says the following:

Please make sure the --ref input matches the build used for the input in --reads.

That means that I need to use the same reference genome for this variant calling command as the one that was used for creating the sequencing file I use as input in that command? If so, is there a way to find which genome was used for creating the sequencing file?

[iraun]

Try checking the header of the BAM file to see which reference genome was used for the alignment step (because I guess you have a bam file?):

samtools view -H FILE.bam