Mercurial > repos > ryanmorin > nextgen_variant_identification

*** SNVMix2 ***

This version of SNVMix2 has has been tested under Linux and Mac OS X.

To build:

> unzip -x ../SNVMix2-v{VERSION}.zip
> cd SNVmix2-v{VERSION}/
> make

Binary file is called "SNVMix2", for help run with -h flag

> ./SNVMix2 -h

You can copy that file to a preferred location.

SNVMix2 defaults to reading from standard input if flag '-i' is not specified,
so you can use it in pipe mode next to a MAQ or samtools pileup command, saving
storage space. Same applies for standard output and the "-o" flag while Classifying.

Parameter '-m <file>' is used to read the model parameters when Classifying (-C)
or write them in Train mode (-T)

Different models for base and mapping qualities are available using the "-t" flag,
SNVMix1 mode can be accessed by selecting "-t SNVMix1"

Pileup file should be generated with base and mapping qualities but without consensus,
such as the one obtained when running, with samtools-0.1.4:
	samtools pileup -s -l <in_list.txt> -f <ref.fa> <in.bam>

or with maq-0.7.0:
	maq pileup -v <ref.bfa> <in.map>


A perl script is provided to filter SNVMix2 result according to a specified
threshold, help on this script can be found running:

> ./misc/snvmix2summary.pl -h

This script can filter candidate SNVs using two methods specified by the '-c <TYPE>'
flag:

'-c 2'	Will consider only two classes, either homozygote for the reference allele
	( p(AA) ) or not ( p(AB) + p(BB) )

'-c 3'	Will consider the three clases p(AA), p(AB), p(BB) separately


The output still still retains the unmodified probability values, so p_AB can still
be distinguished from p_BB in case '-c 2' is used.


Notes:

A working gcc compiler is needed and under Linux libc >= 4.6.27 is required.

Be careful if you copy & paste pileup files, as some text editors tend to change
"tabs" for spaces, which is needed as the field delimiter. This can cause problems
in the parser.

//
Comments and Questions:
Sohrab Shah	sshah@bccrc.ca
Rodrigo Goya	rgoya@bcgsc.ca

//
LICENSE: this software is distributed under the MIT license
author	ryanmorin
date	Wed, 12 Oct 2011 19:50:38 -0400
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