Nextflow pipeline for coverage computation with samtools mpileup (bed parallelization)
Command line example:
nextflow run iarcbioinfo/mpileup-nf --bam_folder BAM/ --fasta_ref ref.fasta --bedfile bedfile.bed --nsplit 100 --out_table output.txt
Output tab-delimited file looks like:
chr pos K211007X K211008Y K211010Z
chr1 801957 314 252 287
chr1 866511 212 128 169
with samples in columns and positions in lines.