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Bed File Bedpe Format

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Hi,

I'm having trouble with converting the bam file into bed -bedpe using the bedtools.

workflow:
samtools sort -n mut.bam mut.Namesorted
bamTobed -i mut.Namesorted.bam -bedpe > dilpMerged_bedpe.bed

After sorting the file by read name (option -n) I run the bamTobed command. but it gives me an error message after running a few lines:

*ERROR: -bedpe requires BAM to be sorted/grouped by query name.

What am I doing wrong here?

Thanks

A.


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