Issues with BedToIntervalList Picard tool
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19 months ago
Elisa • 0

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:

How can I solve this issue?

Picard • 741 views
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19 months ago

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

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

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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.