Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/README @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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1 *** SNVMix2 *** | |
2 | |
3 This version of SNVMix2 has has been tested under Linux and Mac OS X. | |
4 | |
5 To build: | |
6 | |
7 > unzip -x ../SNVMix2-v{VERSION}.zip | |
8 > cd SNVmix2-v{VERSION}/ | |
9 > make | |
10 | |
11 Binary file is called "SNVMix2", for help run with -h flag | |
12 | |
13 > ./SNVMix2 -h | |
14 | |
15 You can copy that file to a preferred location. | |
16 | |
17 SNVMix2 defaults to reading from standard input if flag '-i' is not specified, | |
18 so you can use it in pipe mode next to a MAQ or samtools pileup command, saving | |
19 storage space. Same applies for standard output and the "-o" flag while Classifying. | |
20 | |
21 Parameter '-m <file>' is used to read the model parameters when Classifying (-C) | |
22 or write them in Train mode (-T) | |
23 | |
24 Different models for base and mapping qualities are available using the "-t" flag, | |
25 SNVMix1 mode can be accessed by selecting "-t SNVMix1" | |
26 | |
27 Pileup file should be generated with base and mapping qualities but without consensus, | |
28 such as the one obtained when running, with samtools-0.1.4: | |
29 samtools pileup -s -l <in_list.txt> -f <ref.fa> <in.bam> | |
30 | |
31 or with maq-0.7.0: | |
32 maq pileup -v <ref.bfa> <in.map> | |
33 | |
34 | |
35 A perl script is provided to filter SNVMix2 result according to a specified | |
36 threshold, help on this script can be found running: | |
37 | |
38 > ./misc/snvmix2summary.pl -h | |
39 | |
40 This script can filter candidate SNVs using two methods specified by the '-c <TYPE>' | |
41 flag: | |
42 | |
43 '-c 2' Will consider only two classes, either homozygote for the reference allele | |
44 ( p(AA) ) or not ( p(AB) + p(BB) ) | |
45 | |
46 '-c 3' Will consider the three clases p(AA), p(AB), p(BB) separately | |
47 | |
48 | |
49 The output still still retains the unmodified probability values, so p_AB can still | |
50 be distinguished from p_BB in case '-c 2' is used. | |
51 | |
52 | |
53 | |
54 | |
55 | |
56 Notes: | |
57 | |
58 A working gcc compiler is needed and under Linux libc >= 4.6.27 is required. | |
59 | |
60 Be careful if you copy & paste pileup files, as some text editors tend to change | |
61 "tabs" for spaces, which is needed as the field delimiter. This can cause problems | |
62 in the parser. | |
63 | |
64 // | |
65 Comments and Questions: | |
66 Sohrab Shah sshah@bccrc.ca | |
67 Rodrigo Goya rgoya@bcgsc.ca | |
68 | |
69 // | |
70 LICENSE: this software is distributed under the MIT license |