subread

Version:: 2.0.3
Category:: bio
Cluster:: Loki

Author / Distributor

http://subread.sourceforge.net/

Description

High performance read alignment, quantification and mutation discovery for processing next-generation sequencing data.

Documentation

Usage:

 ./exactSNP [options] -i input -g reference_genome -o output

Required arguments:

 -i <file>  Specify name of an input file including read mapping results. The
[-b if BAM] format of input file can be SAM or BAM (-b needs to be specified
            if a BAM file is provided).

 -g <file>  Specify name of the file including all reference sequences. Only
            one single FASTA format file should be provided.

 -o <file>  Specify name of the output file. This program outputs a VCF format
            file that includes discovered SNPs.

Optional arguments:

 -a <file>  Provide a set of annotated SNPs (e.g. SNPs included in the dbSNP
            database). The supplied file should be in VCF format (gzipped file
            is accepted). Providing known SNPs to the program should improve
            its SNP calling performance. Note that the provided SNPs may or
            may not be called.

 -b         Indicate the input file provided via -i is in BAM format.

 -Q <int>   Specify the q-value cutoff for SNP calling at sequencing depth of
            50X. 12 by default. The corresponding p-value cutoff is 10^(-1*Q).
            Note that this program automatically adjusts the q-value cutoff
            according to the sequencing depth at each chromosomal location.

 -f <float> Specify the minimum fraction of mis-matched bases a SNP-containing
            location must have. Its value must between 0 and 1. 0 by default.

 -n <int>   Specify the minimum number of mis-matched bases a SNP-containing
            location must have. 1 by default.

 -r <int>   Specify the minimum number of mapped reads a SNP-containing
            location must have (ie. the minimum coverage). 1 by default.

 -x <int>   Specify the maximum depth a SNP location is allowed to have.
            1,000,000 reads by default. This option is useful for removing PCR
            artefacts.

 -s <int>   Specify the minimum base quality scores (Phred scores) read bases
            must satisfy to be used for SNP calling. 13 by default. Read bases
            with quality scores less than 13 will be excluded from the
            analysis.

 -t <int>   Specify the number of bases trimmed off from each end of the read.
            3 by default.

 -T <int>   Specify the number of threads. 1 by default.

 -v         output version of the program.

 -C <path>  Specify the path to save the temporary files.

Examples/Usage

List available modules:
```
$ module avail subread
```
Load the subread module:
```
$ module load bio/Subread/2.0.3
```
Check the loaded modules:
```
$ module list
```
Unload the subread module:
```
$ module unload bio/Subread/2.0.3
```
Indicate the input file provided via -i is in BAM format:
```
$ exactSNP -b
```
Specify name of the file including all reference sequences. Only one single FASTA format file should be provided:
```
$ exactSNP -g <file>
```

Installation

Source code is obtained from Subread