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