Difference between revisions of "Samtools"
(Created page with "Installed in /apps/samtools/0.1.16") |
|||
| (20 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | + | __NOTOC__ | |
| + | __NOEDITSECTION__ | ||
| + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] | ||
| + | {|<!--Main settings - REQUIRED--> | ||
| + | |{{#vardefine:app|samtools}} | ||
| + | |{{#vardefine:url|http://samtools.sourceforge.net/}} | ||
| + | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
| + | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
| + | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| + | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
| + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
| + | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
| + | |} | ||
| + | <!-- ######## Template Body ######## --> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| + | |||
| + | 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. | ||
| + | <!--Modules--> | ||
| + | ==Environment Modules== | ||
| + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_SAMTOOLS_BIN - executable directory | ||
| + | {{#if: {{#var: exe}}|==How To Run== | ||
| + | See "man samtools" for a command line version of the samtools help. | ||
| + | |}} | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
| + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| + | {{#if: {{#var: policy}}|==Usage Policy== | ||
| + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
| + | {{#if: {{#var: testing}}|==Performance== | ||
| + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | ||
| + | {{#if: {{#var: faq}}|==FAQ== | ||
| + | *'''Q:''' **'''A:'''|}} | ||
| + | {{#if: {{#var: citation}}|==Citation== | ||
| + | If you publish research that uses {{{app}}} you have to cite it as follows: | ||
| + | WRITE CITATION HERE | ||
| + | |}} | ||
Latest revision as of 22:04, 21 August 2022
Description
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