Awesome
bametrics-nf
Nextflow pipeline to compute average metrics from reads that overlap a given set of positions
Dependencies
-
Install nextflow.
curl -fsSL get.nextflow.io | bashAnd move it to a location in your
$PATH(/usr/local/binfor 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 |