Freebayes 'bamleftalign' function usage issues (Part of the 'Du Novo' Sequencing pipeline)

Question

[jmath97]

Hi,

I've been trying to use the 'Du Novo' sequencing pipeline to analyze a set of bacterial whole genome sequencing data. This is the paper outlining the method: Streamlined analysis of duplex sequencing data with Du Novo. At the 9th step, the pipeline suggests using a function from the package 'freebayes' called 'bamleftalign'. I've tried using this function as I've listed below.

bamleftalign duplex.filt.aln.sort.bam -f ref.fasta > output.bam

For some reason, it doesn't provide an output -- it leaves the output.bam file empty. Is there something wrong with my usage of the function?

Is there something else that I should be checking? I checked the function in my PATH and I've ran and passed the freebayes package test files.

Any and all input would be appreciated!

Answer 1

[jmath97]

For any other users that might have this question, I realized my usage was incorrect. The function requires piping the bam input file into the function as opposed to taking the bam file as a standard input.

cat duplex.filt.aln.sort.bam | bamleftalign -f ref.fasta > duplex.filt.aln.sort.leftalign.bam