FileFormat bam

Bam files are binary alignment files, and are generated after raw reads in fastq format are aligned to a reference genome or other reference sequence. 4DN pipelines use bwa-mem to align and generate bams, while the ENCODE pipelines may use bowtie2. When bam files are indexed, there may also be a corresponding .bai file generated. Samtools can be used to convert between bam and the non-binary sam format.