Difference between revisions of "Applications/Samtools"
From HPC
m |
m (→Navigation) |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 14: | Line 14: | ||
* '''BCFtools''' - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants | * '''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 | * '''HTSlib''' - A C library for reading/writing high-throughput sequencing data | ||
| + | |||
| + | |||
| + | With linkages to the following modules too: | ||
| + | |||
| + | |||
| + | * [[applications/Bowtie1|Bowtie1]] | ||
| + | * [[applications/Bowtie2|Bowtie2]] | ||
| + | * [[applications/Cufflinks|Cufflinks]] | ||
| + | * [[applications/Tophat|Tophat]] | ||
| + | |||
| + | |||
| Line 76: | Line 87: | ||
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module samtools/gcc/1.3.1 | + | [username@login01 ~]$ module samtools/gcc/1.3.1 |
</pre> | </pre> | ||
| Line 83: | Line 94: | ||
==Further Information== | ==Further Information== | ||
| − | [http://www.htslib.org/ http://www.htslib.org/] | + | * [http://www.htslib.org/ http://www.htslib.org/] |
| + | |||
| + | {{Modulepagenav}} | ||
Latest revision as of 10:58, 16 November 2022
Application Details
- Description: The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information
- Version: 1.3.1.
- Module: module samtools/gcc/1.3.1.
- Licence: BSD License, MIT License
Usage Areas
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
With linkages to the following modules too:
Usage Examples
Some usage examples of Samtools are listed below:
Index the reference FASTA.
[username@login01 ~]$ samtools faidx ex1.fa
Convert the (headerless) SAM file to BAM. Note if we had used "samtools view -h" above to create the ex1.sam.gz then we could omit the "-t ex1.fa.fai" option here.
[username@login01 ~]$ samtools view -S -b -t ex1.fa.fai -o ex1.bam ex1.sam.gz
Build an index for the BAM file:
[username@login01 ~]$ samtools index ex1.bam
View a portion of the BAM file:
[username@login01 ~]$ samtools view ex1.bam seq2:450-550
Visually inspect the alignments at the same location:
[username@login01 ~]$ samtools tview -p seq2:450 ex1.bam ex1.fa
View the data in pileup format:
[username@login01 ~]$ samtools mpileup -f ex1.fa ex1.bam
Generate an uncompressed VCF file of variants:
[username@login01 ~]$ samtools mpileup -vu -f ex1.fa ex1.bam > ex1.vcf
Generate a compressed VCF file of variants:
[username@login01 ~]$ samtools mpileup -g -f ex1.fa ex1.bam > ex1.bcf
Module
[username@login01 ~]$ module samtools/gcc/1.3.1