I'm trying to convert a bed file into interval list format. I'm not sure about which file I should choose as SD. I've tried using 'genome.dict' (genome.fa is the reference genome I've used to align) or the BAM file of the aligned reads; in both cases I get the following error:
Exception in thread "main" picard.PicardException: Sequence 'chr1_KI270763v1_alt' was not found in the sequence dictionary
How can I solve this issue?
Thanks in advance