Oakley

VCFtools

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

Availability and Restrictions

The following versions of VCFtools are available on OSC clusters:

bcftools

bcftools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

Availability and Restrictions

The following versions of bcftools are available on OSC clusters:

VarScan

VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.

Availability and Restrictions

The following versions of VarScan are available on OSC clusters:

MuTect

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Availability and Restrictions

The following versions of MuTect are available on OSC clusters:

Picard

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Availability and Restrictions

The following versions of Picard are available on OSC clusters:

SAMtools

SAM format is a generic format for storing large nucleotide sequence alignments. SAMtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Availability and Restrictions

The following versions of SAMtools are available on OSC clusters:

GATK

GATK is a software package for analysis of high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

Availability and Restrictions

The following versions of GATK are available on OSC clusters:

BWA

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

Availability and Restrictions

The following versions of BWA are available on OSC clusters:

Bowtie1

Bowtie1 is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Availability and Restrictions

The following versions of Bowtie1 are available on OSC clusters:

bedtools

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. While each individual tool is designed to do a relatively simple task, quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Availability and Restrictions

The following versions of bedtools are available on OSC clusters:

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