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comparison vcfvcfintersect.xml @ 1:fabee003a629 draft default tip

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author anton
date Wed, 11 Jun 2014 16:42:03 -0400
parents 1457784cf167
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0:1457784cf167 1:fabee003a629
81 <param name="isect_union" value="Intersect" /> 81 <param name="isect_union" value="Intersect" />
82 <param name="invert" value="False" /> 82 <param name="invert" value="False" />
83 <param name="loci" value="False" /> 83 <param name="loci" value="False" />
84 <patam name="adv_options" value="False" /> 84 <patam name="adv_options" value="False" />
85 <param name="window_size" value="30" /> 85 <param name="window_size" value="30" />
86 <param name="ref_file" value="vcflib-human-reference-chr20-XY.fa" /> 86 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
87 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> 87 <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>
88 </test> 88 </test>
89 <test> 89 <test>
90 <param name="reference_source_selector" value="history" /> 90 <param name="reference_source_selector" value="history" />
91 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> 91 <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
93 <param name="isect_union" value="Union" /> 93 <param name="isect_union" value="Union" />
94 <param name="invert" value="False" /> 94 <param name="invert" value="False" />
95 <param name="loci" value="False" /> 95 <param name="loci" value="False" />
96 <patam name="adv_options" value="False" /> 96 <patam name="adv_options" value="False" />
97 <param name="window_size" value="30" /> 97 <param name="window_size" value="30" />
98 <param name="ref_file" value="vcflib-human-reference-chr20-XY.fa" /> 98 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
99 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/> 99 <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
100 </test> 100 </test>
101 </tests> 101 </tests>
102 <help> 102 <help>
103 103
104 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp. 104 Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp.
105 105
106 Options:: 106 The options are::
107 107
108 -v, --invert invert the selection, printing only records which would 108 -v, --invert invert the selection, printing only records which would
109 -i, --intersect-vcf FILE use this VCF for set intersection generation 109 -i, --intersect-vcf FILE use this VCF for set intersection generation
110 -u, --union-vcf FILE use this VCF for set union generation 110 -u, --union-vcf FILE use this VCF for set union generation
111 -w, --window-size N compare records up to this many bp away (default 30) 111 -w, --window-size N compare records up to this many bp away (default 30)