Issues with BedToIntervalList Picard tool

Question

[Elisa]

Hi everyone,

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

Answer 1

[Pierre Lindenbaum]

Sequence 'chr1_KI270763v1_alt' was not found in the sequence dictionary

your bed file contains a chromosome "chr1_KI270763v1_alt" that is not defined in the REFERENCE/DICT file. if you're not interested with that contig, you can just remove it from your bed with grep -v

[Elisa]

I'm interested with that contig so I can't remove it. Is it allowed to add that contig to the reference genome?

[Pierre Lindenbaum]

it depends of your downstream analysis. For example if you're using a bam and gatk, the internal dictionary should be the very same than the reference sequence.