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1 <tool id="VCFStorage" name="VCFStorage" version="0.01">
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2 <description> stores info from variant calling into a table. It will create a tabulate filed with SNP infos</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">VCF_Gandalf_Tools</requirement>
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5 </requirements>
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6 <version_command>
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7 VCFStorage.py --version
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8 </version_command>
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9 <command interpreter="python">
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10 VCFStorage_wrapper.py -f $inputFasta -o $outputVCFStorage
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11 ## genome list
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12 #for $VCF in $VCFFile
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13 -l $VCF.strainName
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14 -L $VCF.inputStrainVCF
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15 #end for
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16 </command>
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17 <inputs>
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18 <param name="inputFasta" type="data" format="fasta" label="Input genome sequence file name (fasta)"/>
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19 <repeat name="VCFFile" title="VCF list" min="1">
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20 <param name="strainName" size="20" type="text" value="V1" label="strain name (no space allowed)"/>
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21 <param name="inputStrainVCF" type="data" format="vcf" label="Select VCF file "/>
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22 </repeat>
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23 </inputs>
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24 <outputs>
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25 <data format="tabular" name="outputVCFStorage" label="${tool.name} on ${on_string} (tabular)"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="inputFasta" ftype="fasta" value="chr17.fa" />
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30 <param name="strainName" value="V1"/>
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31 <param name="inputStrainVCF" ftype="vcf" value="chr17.VCF"/>
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32 <output name="outputVCFStorage" ftype="tabular" file="Expchr17.tab"/>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **stores info from variant calling into a table. It will create a tabulate filed with SNP infos**
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37
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38 -----
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39
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40 **what it does :**
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41
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42 VCFStorage.py is a python script that allows to store data from multiple VCF into a single tabular marker file. each VCF will be a new column on the final output.
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43
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44 -----
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45
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46 **input format :**
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47
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48 Multiple files are necessary as input :
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49
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50 - the fasta file of your genomic sequence
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51 - multiple VCF files (1 per strain). It is strongly advised to use the column filter (col 7) for filtered positions instead of removing the lines from the VCF.
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52
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53 -----
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54
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55 **ouput format :**
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56
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57 the result is a tab delimited format file where all genomic positions are in rows, and all strains are in columns (in the order you gave the VCF)
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58
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59 For each position and each genome, a code is attributed :
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60
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61 - for the reference : ::
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62
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63 A,T,G,C for the corresponding nucleotidic acid
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64
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65 - for the genomes : ::
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66
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67 U if the position was not refered in the VCF file
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68 R if the base is similar to the reference
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69 F if the base has been filtered in the column FILTER (column 7) of the VCF
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70 A,T,G,C if the genome has a validated SNP at the position
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71
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72
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73 -----
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74
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75 **example :**
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76
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77 fasta input file (genomic sequence): ::
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78
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79 >chr_17
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80 ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa
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81 TACGCGCGCGCCTAACCCTACGACTTTAACCTACTCTAAACTCTCCTACTAGTACGTCTT
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82
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83 VCF input file : ::
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84
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85 ##fileformat=VCFv4.1
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86 ##fileDate=20140725
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87 ##source=freeBayes v0.9.13-2-ga830efd
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88 ##reference=exmple.fsa
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89 ##phasing=none
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90 ##DetectedFormat=freebayes
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91 ##FILTER=<ID=G_AN,Description="The SNP has been filtered ; out of AN range(over 2)">
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92 ##FILTER=<ID=G_AF,Description="The SNP has been filtered ; out of AF range(under 0.9)">
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93 ##FILTER=<ID=G_DP,Description="The SNP has been filtered ; out of DP range(15 - 35)">
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94 ##FILTER=<ID=InDel,Description="The SNP has been filtered ; InDel detected">
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95 ##FILTER=<ID=Nmatch,Description="The SNP has been filtered ; reference base detected : N">
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96 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V1
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97 chr_17 17 . A G 529.213 G_AF;G_DP AB=0.583333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=21;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.1137;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=751;QR=535;RO=15;RPP=5.59539;RPPR=4.31318;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=5;SRP=6.62942;SRR=10;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.58;G_DP=36;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:36:15:535:21:751:-10,0,-10
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98 chr_17 37 . C G 1082.38 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=34;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=3.26577;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=48.0391;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1243;QR=0;RO=0;RPP=15.5282;RPPR=0;RUN=1;SAF=18;SAP=3.26577;SAR=16;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=34;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:34:0:0:34:1243:-10,-9.23017,0
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99 chr_17 40 . T T 825.518 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=29;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=6.67934;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.92992;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1082;QR=178;RO=5;RPP=9.07545;RPPR=13.8677;RUN=1;SAF=13;SAP=3.68421;SAR=16;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.85;G_DP=34;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:34:5:178:29:1082:-10,0,-6.82575
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100 chr_17 60 . A . 699.741 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=17.2236;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=32.2544;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=823;QR=0;RO=0;RPP=9.32731;RPPR=0;RUN=1;SAF=12;SAP=3.40511;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=22;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:22:0:0:22:823:-10,-5.98732,0
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101 chr_17 73 . T . 846.299 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=27;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=16.6021;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=38.84;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1002;QR=0;RO=0;RPP=5.02092;RPPR=0;RUN=1;SAF=21;SAP=21.1059;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=27;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:27:0:0:27:1002:-10,-7.34226,0
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102 chr_17 81 . C T 764.464 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=25;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=13.5202;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=36.1324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=902;QR=0;RO=0;RPP=3.79203;RPPR=0;RUN=1;SAF=19;SAP=17.6895;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=25;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:25:0:0:25:902:-10,-6.76842,0
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103 chr_17 105 . C T 1154 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=37;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.88603;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=52.0047;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1336;QR=0;RO=0;RPP=19.9713;RPPR=0;RUN=1;SAF=23;SAP=7.76406;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=37;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:37:0:0:37:1336:-10,-10,0
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104 chr_17 112 . G A 1276.25 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=10.8276;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=55.9501;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1471;QR=0;RO=0;RPP=10.8276;RPPR=0;RUN=1;SAF=26;SAP=10.8276;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=40;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1471:-10,-10,0
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105
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106 expected result : ::
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107
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108 CHROM POS reference V1
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109 chr_17 1 C U
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110 chr_17 2 C U
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111 chr_17 3 C U
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112 chr_17 4 T U
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113 chr_17 5 A U
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114 chr_17 6 A U
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115 chr_17 7 C U
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116 chr_17 8 C U
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117 chr_17 9 C U
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118 chr_17 10 T U
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119 chr_17 11 A U
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120 chr_17 12 A U
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121 chr_17 13 C U
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122 chr_17 14 C U
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123 chr_17 15 C U
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124 chr_17 16 T U
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125 chr_17 17 A F
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126 chr_17 18 A U
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127 chr_17 19 C U
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128 chr_17 20 C U
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129 chr_17 21 C U
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130 chr_17 22 T U
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131 chr_17 23 A U
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132 chr_17 24 A U
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133 chr_17 25 C U
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134 chr_17 26 C U
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135 chr_17 27 C U
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136 chr_17 28 T U
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137 chr_17 29 A U
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138 chr_17 30 A U
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139 chr_17 31 C U
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140 chr_17 32 C U
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141 chr_17 33 C U
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142 chr_17 34 T U
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143 chr_17 35 A U
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144 chr_17 36 A U
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145 chr_17 37 C G
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146 chr_17 38 C U
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147 chr_17 39 C U
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148 chr_17 40 T F
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149 chr_17 41 A U
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150 chr_17 42 A U
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151 chr_17 43 C U
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152 chr_17 44 C U
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153 chr_17 45 C U
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154 chr_17 46 T U
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155 chr_17 47 A U
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156 chr_17 48 A U
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157 chr_17 49 C U
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158 chr_17 50 C U
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159 chr_17 51 C U
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160 chr_17 52 T U
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161 chr_17 53 A U
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162 chr_17 54 A U
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163 chr_17 55 C U
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164 chr_17 56 C U
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165 chr_17 57 C U
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166 chr_17 58 T U
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167 chr_17 59 A U
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168 chr_17 60 A R
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169 chr_17 61 T U
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170 chr_17 62 A U
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171 chr_17 63 C U
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172 chr_17 64 G U
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173 chr_17 65 C U
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174 chr_17 66 G U
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175 chr_17 67 C U
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176 chr_17 68 G U
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177 chr_17 69 C U
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178 chr_17 70 G U
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179 chr_17 71 C U
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180 chr_17 72 C U
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181 chr_17 73 T R
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182 chr_17 74 A U
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183 chr_17 75 A U
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184 chr_17 76 C U
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185 chr_17 77 C U
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186 chr_17 78 C U
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187 chr_17 79 T U
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188 chr_17 80 A U
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189 chr_17 81 C T
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190 chr_17 82 G U
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191 chr_17 83 A U
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192 chr_17 84 C U
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193 chr_17 85 T U
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194 chr_17 86 T U
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195 chr_17 87 T U
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196 chr_17 88 A U
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197 chr_17 89 A U
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198 chr_17 90 C U
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199 chr_17 91 C U
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200 chr_17 92 T U
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201 chr_17 93 A U
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202 chr_17 94 C U
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203 chr_17 95 T U
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204 chr_17 96 C U
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205 chr_17 97 T U
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206 chr_17 98 A U
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207 chr_17 99 A U
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208 chr_17 100 A U
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209 chr_17 101 C U
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210 chr_17 102 T U
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211 chr_17 103 C U
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212 chr_17 104 T U
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213 chr_17 105 C F
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214 chr_17 106 C U
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215 chr_17 107 T U
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216 chr_17 108 A U
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217 chr_17 109 C U
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218 chr_17 110 T U
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219 chr_17 111 A U
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220 chr_17 112 G F
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221 chr_17 113 T U
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222 chr_17 114 A U
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223 chr_17 115 C U
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224 chr_17 116 G U
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225 chr_17 117 T U
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226 chr_17 118 C U
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227 chr_17 119 T U
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228 chr_17 120 T U
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229
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230 -----
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231
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232 **reference :**
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233
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234 ]]>
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235 </help>
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236 </tool>
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