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+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/README	Wed Oct 12 19:50:38 2011 -0400
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+*** 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