IARCbioinfo/bametrics-nf

Nextflow pipeline to compute average metrics from reads that overlap a given set of positions

bametrics-nf

Nextflow pipeline to compute average metrics from reads that overlap a given set of positions

Dependencies

1. Install nextflow.

   curl -fsSL get.nextflow.io | bash

   And move it to a location in your $PATH (/usr/local/bin for example here):

   sudo mv nextflow /usr/local/bin

Input files and options

Command line example:

nextflow run bametrics.nf --bam_folder BAM/ --input_positions positions_by_sample.txt --output_file bametrics_output.txt

Options:

Parameter	Default value	Description
	required
bam_folder	-	Folder containing BAM for each sample you want metrics on position
input_positions	-	File containing position-sample, in line-form "chr pos sample"
	optional
nb_chunks	1	Value defining the number of parallelized processed chunks
output_file	bametrics_output.txt	File name of the output
out_folder	.	Output directory
metrics	"AS"	List of bam metrics, comma delimited

Pipeline execution DAG