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abra2 error java.lang.NumberFormatException

Hello, I have constructed a graph-based pan-genome using MC, and then I used VG to align short-read data to the pan-genome. When I used abra2, the following error occurred. What could be the reason for this??

error

abra2 pangenome java
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written by chiyong4783 • chiyong4783

1 answer

inputs need to be sorted and indexed. can you confirm you are doing this?

samtools sort input.bam -o sorted.bam
samtools index sorted.bam

or some such should result in a .bai index file

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written by phage1 • phage1

I encountered an issue while replacing the BAM file header. Thank you for your comment.

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written by chiyong4783 • chiyong4783

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