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Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [2] it consists of the lossless, compressed binary representation of the Sequence Alignment Map -files. [3][4] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [5] .

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You can also use the cool Data Slicer app to retrieve subset of data from 1000 genomes BAM files. Command-line utility documentation here and web-app here. Using Data Slicer you can import BAM files on-the fly to your web app.

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A BAM file is just a SAM file but stored in binary format; you should always convert your SAM files into BAM format since they are smaller in size and are faster to manipulate.

A bam file is a binary blob that stores all of your aligned sequence data. You can view what's in the bam file using "samtools view bamfile.bam | less". Bam files can also have a companion file, called an index file. This file has the same name, suffixed with .bai.

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