C CPP

In the past week, I’ve been adapting my own HiC pipeline to the 4DN recommended pipeline. One critical step is to convert hundreds of read-paired BAM files generated by my old pipeline to pairs format. 4DN consortium provides a tool, bam2pairs, for this task. It’s basically a Perl script that calls Samtools to read a BAM file and output targeted fields. Because the pair format suggests the columns to be sorted by chr1-chr2-pos1-pos2, bam2pairs then calls Linux “sort” to perform four times of sorting based on these four columns [1]. [Read More]