comparison intersect_snp.xml @ 0:3edc7bb490d3 draft default tip

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0:3edc7bb490d3

<tool id="intersect_snp" name="intersect_snp" version="0">
  <description>tool for snp VCF file intersection </description>
  <requirements>
  </requirements>
  <command>
	perl  $__tool_directory__/14_june_18_intersect.snps.with.infos.pl
  $input1 $input2 $input3 intersect 2>log
  </command>
  <inputs>
    <param name="input1" format="vcf" type="data" label="VCF File" help="Varscan2 snp output" />
    <param name="input2" format="vcf" type="data" label="VCF File" help="Frebayes snp output" />
    <param name="input3" format="vcf" type="data" label="VCF File" help="GATK HaplotypeCaller snp output" />
  </inputs>
  <outputs>
    <data format="vcf" name="output1" from_work_dir="intersect.common.snps.vcf" label="${tool.name} on ${on_string} common snps" />
    <data format="vcf" name="output2" from_work_dir="intersect.unique.snps.vcf" label="${tool.name} on ${on_string} unique snps" />
    <data format="txt" name="output3" from_work_dir="log" label="${tool.name} on ${on_string} log" />
  </outputs>
  <stdio>
  </stdio>
  <help>
**WHAT IT DOES**

Predictions of SNPs from Varscan2, GATK and Freebayes are consolidated into a single call-set following a simple majority consensus rule. Variants  identified by at least two methods are incorporated into a final “high confidence” call set.Singleton variants predicted by only one method are considered less reliable and are included in a low quality call-set.

**The final output consists in two VCF files:**

-SNPs common to at least 2 methods

-Singleton SNPs obtained from a single method

  </help>
  <citations>
       <citation type="doi">10.1186/s12864-018-4508-1</citation>
  </citations>
  <tests>
    <test>
    </test>
  </tests>

</tool>