Difference between revisions of "Samtools"

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__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]
<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|samtools}}
 
|{{#vardefine:app|samtools}}
 
|{{#vardefine:url|http://samtools.sourceforge.net/}}
 
|{{#vardefine:url|http://samtools.sourceforge.net/}}
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|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
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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.
 
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.
'''Note:''' The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software.
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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.
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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.
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Execution Environment and Modules==
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==Environment Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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==System Variables==
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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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{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

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