Difference between revisions of "Applications/Samtools"
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Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: | 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 | + | * '''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 | + | * '''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 |
+ | ===Usage Examples=== | ||
+ | Some usage examples of Samtools are listed below: | ||
+ | Index the reference FASTA. | ||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ samtools faidx ex1.fa | ||
+ | </pre> | ||
+ | |||
+ | 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. | ||
+ | |||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ samtools view -S -b -t ex1.fa.fai -o ex1.bam ex1.sam.gz | ||
+ | |||
+ | Build an index for the BAM file: | ||
+ | |||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ samtools index ex1.bam | ||
+ | </pre> | ||
+ | |||
+ | View a portion of the BAM file: | ||
+ | |||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ samtools view ex1.bam seq2:450-550 | ||
+ | </pre> | ||
+ | |||
+ | Visually inspect the alignments at the same location: | ||
+ | |||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ samtools tview -p seq2:450 ex1.bam ex1.fa | ||
+ | </pre> | ||
+ | |||
+ | View the data in pileup format: | ||
+ | |||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ samtools mpileup -f ex1.fa ex1.bam | ||
+ | </pre> | ||
+ | Generate an uncompressed VCF file of variants: | ||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ samtools mpileup -vu -f ex1.fa ex1.bam > ex1.vcf | ||
+ | </pre> | ||
− | + | Generate a compressed VCF file of variants: | |
<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 ~]$ | + | [username@login01 ~]$ samtools mpileup -g -f ex1.fa ex1.bam > ex1.bcf |
</pre> | </pre> | ||
− | |||
− | |||
+ | ===Module=== | ||
+ | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
+ | [username@login01 ~]$ module samtools/gcc/1.3.1. | ||
</pre> | </pre> | ||
Revision as of 11:56, 24 March 2017
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
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: <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> [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.