Difference between revisions of "Samtools"

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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]
 
{|<!--Main settings - REQUIRED-->
 
{|<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|samtools}}
 
|{{#vardefine:app|samtools}}
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'''Note:''' The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software as well as the '''bcftools''' program.
 
'''Note:''' The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software as well as the '''bcftools''' program.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
[[Modules|modules documentation]]
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
*{{#var:app}}
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_SAMTOOLS_BIN - executable directory
 
* HPC_SAMTOOLS_BIN - executable directory
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
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WRITE CITATION HERE
 
WRITE CITATION HERE
 
|}}
 
|}}
=Validation=
 
* Validated 4/5/2018
 

Latest revision as of 22:04, 21 August 2022

Description

samtools website  

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Bcftools does the SNP calling. It can also concatenate BCF files, index BCFs for fast random access and convert BCF to VCF. In addition, bcftools can operate on some VCFs (e.g. calling SNPs from GL-tagged VCFs), but not for all VCFs; VCF to BCF conversion is not working at the moment, either.

Note: The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software as well as the bcftools program.

Environment Modules

Run module spider samtools to find out what environment modules are available for this application.

System Variables

  • HPC_SAMTOOLS_DIR - installation directory
  • HPC_SAMTOOLS_BIN - executable directory