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Index of /examples/archive/bioinfo/samtools

 October 7, 2021


Index of /examples/archive/bioinfo/samtools

Samtools/BCFtools/HTSlib

Introduction and Notes

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

  • Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
  • BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
  • HTSlib A C library for reading/writing high-throughput sequencing data

    • The following are the description of the folders under samtools example page:

  • data
     this subfolder holds all the data files used in this examplendex for sequences. The example is for reference sequences, but same command can be used to build other all kinds of sequence index in fasta format
  • faidx
     build index for sequences. The example is for reference sequences, but same command can be used to build other all kinds of sequence index in fasta format
  • sam2bam convert SAM to BAM file

    • Further Resources:

    For more information on how to use the software, please visit SAMtools website:


  • SAMtools —

    www.htslib.org/doc/#manual-pages

  • BCFtools —

    www.htslib.org/doc/bcftools.html

  • HTSfile(HTSlib’s utility) —

    www.htslib.org/doc/htsfile.html

    • Contact Information:

    Research Computing Services: help@scc.bu.edu

    Note: Research Computing Services (RCS) example programs are provided
    “as is” without any warranty of any kind. The user assumes the entire risk of
    quality, performance, and repair of any defects. You are encouraged to copy
    and modify any of the given examples for your own use.

    Read more here: Source link