bedtools genomecov -bg -split -ibam bamfile. error: the input file is not sorted correctly.

Question

[Joe]

Hi there,

I try to run command "bedtools genomecov -bg -split -ibam bamfile" to obtain the bed output, while the error is showed as "Input error: Chromosome * found in non-sequential lines. This suggests that the input file is not sorted correctly." To solve that, I try to sort the bam file using "samtools sort -n bamfile -o sortedfile" and then redo the test. The result have the same error.

Anyone can help? Many thanks!

Joe

Answer 1

[finswimmer]

Hello,

I guess bedtools need the bam file sorted by coordinates and not by readnames as you do with samtools sort -n. And did you use sortedfile for redoing yohr test?

fin swimmer

[Joe]

Hi finswimmer,

Thanks for your comment. It works after sorting the bam file by coordinates.

Joe