However, BAM files are binary files and as such they are compact but not readable by humans. SAM files are text files so humans can read them but they are a lot bigger than the BAM files. Because of their compactness BAM files have become the standard format for storing the results of the mapping of reads to a reference sequence
The BAM Header Viewer allows you to peek inside a BAM header, similar to what you would get if you were to run samtools view -H on the BAM file. (BAM headers include information about the reference genome sequences, read groups, and programs used). When launching this viewer, tick one or more BAM files (*.bam).
BAM files store their header as plain-text SAM headers. However, they additionally store the name and The header is expected to be small, especially when compared to the rest of the file, and thus...
Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and then seeks to the end of the file and checks that an end-of-file (EOF) is present and intact (BAM only).
Nov 03, 2014 · After converting the .bam file into the .sam format, our script extracts a predefined amount of reads, writes them back into a sorted .bam file and finally creates a .bai index file from it. The extraction filters for reads on a given chromosome, with a start position in between a given range.
If you have a single bam file that contains multiple libraries, make sure that the readgroup and library information are properly encoded in the sam/bam header, and in each alignment record, otherwise bam2cfg.pl may fail to produce a correct configuration file. Please follow instructions on SourceForgeto properly format your bam files.
While BAM files contain all sequence data within a file, CRAM files are smaller by taking advantage of an additional external "reference The file begins with a 16-byte header containing the following fields
SAM or BAM input file--OUTPUT -O: null: SAM or BAM file to write merged result to: Optional Tool Arguments--arguments_file  read one or more arguments files and add them to the command line--ASSUME_SORTED -AS: false: If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say ...