Mercurial > repos > elixir-it > covacs_intersect_snps
comparison intersect_snp.xml @ 0:3edc7bb490d3 draft default tip
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| author | elixir-it |
|---|---|
| date | Thu, 08 Nov 2018 12:56:30 -0500 |
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| -1:000000000000 | 0:3edc7bb490d3 |
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| 1 <tool id="intersect_snp" name="intersect_snp" version="0"> | |
| 2 <description>tool for snp VCF file intersection </description> | |
| 3 <requirements> | |
| 4 </requirements> | |
| 5 <command> | |
| 6 perl $__tool_directory__/14_june_18_intersect.snps.with.infos.pl | |
| 7 $input1 $input2 $input3 intersect 2>log | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param name="input1" format="vcf" type="data" label="VCF File" help="Varscan2 snp output" /> | |
| 11 <param name="input2" format="vcf" type="data" label="VCF File" help="Frebayes snp output" /> | |
| 12 <param name="input3" format="vcf" type="data" label="VCF File" help="GATK HaplotypeCaller snp output" /> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="vcf" name="output1" from_work_dir="intersect.common.snps.vcf" label="${tool.name} on ${on_string} common snps" /> | |
| 16 <data format="vcf" name="output2" from_work_dir="intersect.unique.snps.vcf" label="${tool.name} on ${on_string} unique snps" /> | |
| 17 <data format="txt" name="output3" from_work_dir="log" label="${tool.name} on ${on_string} log" /> | |
| 18 </outputs> | |
| 19 <stdio> | |
| 20 </stdio> | |
| 21 <help> | |
| 22 **WHAT IT DOES** | |
| 23 | |
| 24 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. | |
| 25 | |
| 26 **The final output consists in two VCF files:** | |
| 27 | |
| 28 -SNPs common to at least 2 methods | |
| 29 | |
| 30 -Singleton SNPs obtained from a single method | |
| 31 | |
| 32 </help> | |
| 33 <citations> | |
| 34 <citation type="doi">10.1186/s12864-018-4508-1</citation> | |
| 35 </citations> | |
| 36 <tests> | |
| 37 <test> | |
| 38 </test> | |
| 39 </tests> | |
| 40 | |
| 41 </tool> |