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1 <tool id="indel_sam2interval" name="Extract indels" version="1.0.0">
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2 <description>from SAM</description>
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3 <command interpreter="python">
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4 indel_sam2interval.py
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5 --input=$input1
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6 --include_base=$include_base
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7 --collapse=$collapse
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8 --int_out=$output1
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9 #if $ins_out.include_ins_out == "true"
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10 --bed_ins_out=$output2
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11 #else
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12 --bed_ins_out="None"
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13 #end if
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14 #if $del_out.include_del_out == "true"
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15 --bed_del_out=$output3
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16 #else
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17 --bed_del_out="None"
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18 #end if
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19 </command>
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20 <inputs>
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21 <param format="sam" name="input1" type="data" label="Select dataset to convert" />
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22 <param name="include_base" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Include the relevant base(s) for each insertion (and a dash (-) for deletions)" />
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23 <param name="collapse" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Collapse repeated locations onto single line with counts" />
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24 <conditional name="ins_out">
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25 <param name="include_ins_out" type="select" label="Include insertions output bed file?">
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26 <option value="true">Yes</option>
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27 <option value="false">No</option>
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28 </param>
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29 <when value="true" />
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30 <when value="false" />
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31 </conditional>
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32 <conditional name="del_out">
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33 <param name="include_del_out" type="select" label="Include deletions output bed file?">
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34 <option value="true">Yes</option>
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35 <option value="false">No</option>
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36 </param>
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37 <when value="true" />
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38 <when value="false" />
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data format="interval" name="output1" />
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43 <data format="bed" name="output2">
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44 <filter>ins_out[ "include_ins_out" ] == "true"</filter>
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45 </data>
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46 <data format="bed" name="output3">
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47 <filter>del_out[ "include_del_out" ] == "true"</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input1" value="indel_sam2interval_in1.sam" ftype="sam"/>
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53 <param name="include_base" value="true"/>
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54 <param name="collapse" value="true"/>
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55 <param name="include_ins_out" value="true" />
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56 <param name="include_del_out" value="true" />
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57 <output name="output1" file="indel_sam2interval_out1.interval" ftype="interval"/>
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58 <output name="output2" file="indel_sam2interval_out2.bed" ftype="bed"/>
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59 <output name="output3" file="indel_sam2interval_out3.bed" ftype="bed"/>
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60 </test>
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61 </tests>
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62 <help>
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63
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64 **What it does**
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65
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66 Given a SAM file containing indels, converts these to an interval file with a column indicating whether it is an insertion or a deletion, and then also can create a BED file for each type (one for insertions, one for deletions). The interval file can be combined with other like files to create a table useful for analysis with the Indel Analysis Table tool. The BED files can be useful for visualizing the reads.
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67
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68 -----
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69
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70 **Example**
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71
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72 Suppose you have the following mapping results::
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73
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74 r327 16 chrM 11 37 8M1D10M * 0 0 CTTACCAGATAGTCATCA -+<2;?@BA@?-,.+4=4 XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:41^C35
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75 r457 0 chr1 14 37 14M * 0 0 ACCTGACAGATATC =/DF;?@1A@?-,. XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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76 r501 16 chrM 6 23 7M1I13M * 0 0 TCTGTGCCTACCAGACATTCA +=$2;?@BA@?-,.+4=4=4A XT:A:U NM:i:3 X0:i:1 X1:i:1 XM:i:2 XO:i:1 XG:i:1 MD:Z:28C36G9 XA:Z:chrM,+134263658,14M1I61M,4;
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77 r1288 16 chrM 8 37 11M1I7M * 0 0 TCACTTACCTGTACACACA /*F2;?@%A@?-,.+4=4= XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T0T1A69
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78 r1902 0 chr1 4 37 7M2D18M * 0 0 AGTCTCTTACCTGACGGTTATGA <2;?@BA@?-,.+4=4=4AA663 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0
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79 r2204 16 chrM 9 0 19M * 0 0 CTGGTACCTGACAGGTATC 2;?@BA@?-,.+4=4=4AA XT:A:R NM:i:1 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75 XA:Z:chrM,-564927,76M,1;
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80 r2314 16 chrM 6 37 10M2D8M * 0 0 TCACTCTTACGTCTGA <2;?@BA@?-,.+4=4 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:25A5^CA45
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81 r3001 0 chrM 13 37 3M1D5M2I7M * 0 0 TACAGTCACCCTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0
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82 r3218 0 chr1 13 37 8M1D7M * 0 0 TACAGTCACTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0
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83 r4767 16 chr2 3 37 15M2I7M * 0 0 CAGACTCTCTTACCAAAGACAGAC <2;?@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T1A4T65
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84 r5333 0 chrM 5 37 17M1D8M * 0 0 GTCTCTCATACCAGACAACGGCAT FB3$@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:45C10^C0C5C13
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85 r6690 16 chrM 7 23 20M * 0 0 CTCTCTTACCAGACAGACAT 2;?@BA/(@?-,.+4=4=4A XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 XA:Z:chrM,-568532,76M,1;
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86 r7211 0 chrM 7 37 24M * 0 0 CGACAGAGACAAAATAACATTTAA //<2;?@BA@?-,.+4=442;;6: XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:1 MD:Z:73G0G0
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87 r7899 69 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'#
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88 r9192 133 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&%
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89 r9922 16 chrM 4 0 7M3I9M * 0 0 CCAGACATTTGAAATCAGG F/D4=44^D++26632;;6 XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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90 r9987 16 chrM 4 0 9M1I18M * 0 0 AGGTTCTCATTACCTGACACTCATCTTG G/AD6"/+4=4426632;;6:<2;?@BA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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91 r10145 16 chr1 16 0 5M2D7M * 0 0 CACATTGTTGTA G//+4=44=4AA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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92 r10324 16 chrM 15 0 6M1D5M * 0 0 CCGTTCTACTTG A@??8.G//+4= XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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93 r12331 16 chrM 17 0 4M2I6M * 0 0 AGTCGAATACGTG 632;;6:<2;?@B XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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94 r12914 16 chr2 24 0 4M3I3M * 0 0 ACTACCCCAA G//+4=42,. XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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95 r13452 16 chrM 13 0 3M1D11M * 0 0 TACGTCACTCATCA IIIABCCCICCCCI XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76
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96
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97
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98 The following three files will be produced (Interval, Insertions BED and Deletions BED)::
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99
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100 chr1 11 13 D - 1
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101 chr1 21 22 D - 1
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102 chr1 21 23 D - 1
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103 chr2 18 19 I AA 1
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104 chr2 28 29 I CCC 1
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105 chrM 11 12 I TTT 1
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106 chrM 13 14 I C 1
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107 chrM 13 14 I T 1
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108 chrM 16 17 D - 1
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109 chrM 16 18 D - 1
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110 chrM 19 20 D - 1
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111 chrM 19 20 I T 1
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112 chrM 21 22 D - 1
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113 chrM 21 22 I GA 1
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114 chrM 22 23 D - 1
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115
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116 chr2 18 19
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117 chr2 28 29
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118 chrM 11 12
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119 chrM 13 14
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120 chrM 13 14
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121 chrM 19 20
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122 chrM 21 22
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123
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124 chr1 11 13
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125 chr1 21 22
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126 chr1 21 23
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127 chrM 16 17
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128 chrM 16 18
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129 chrM 19 20
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130 chrM 21 22
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131 chrM 22 23
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132
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133 For more information on SAM, please consult the `SAM format description`__.
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134
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135 .. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943
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136
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137
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138 </help>
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139 </tool>
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