FileFormat bam

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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.

   September 18th, 2018 at 2:52am

Details

file_format 
bam
assay_types 
  1. Sequencing
extrafile_formats 
  1. bai
file_content 
alignments
standard_file_extension 
bam
url 
http://samtools.github.io/hts-specs/SAMv1.pdf
valid_item_types 
  1. FileProcessed
  2. FileReference