Mercurial > repos > elixir-it > covacs_intersect_snps
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author | elixir-it |
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date | Thu, 08 Nov 2018 12:56:30 -0500 |
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<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>