I'd like to use reads mapped across all 25 chromosomes of the genome for dibayes as input, but only call variations on chr21. However, I get an error stating that the reference isn't 'the same and contains 25 contigs versus 1' as the reference used to map the .bam files used as input, which was obvious. Is there a way around this or do I have to specifically map to chr21 to then call variations on chr21? Thanks.
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