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author | gandres |
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date | Fri, 11 Dec 2015 07:35:00 -0500 |
parents | 612066e3f57d |
children | 2b6bb9d5e4e9 |
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<tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.1.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> </description> <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="0.1.12b">vcftools</requirement> </requirements> <!-- [STRONGLY RECOMMANDED] Exit code rules --> <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> </stdio> <!-- [REQUIRED] The command to execute --> <command interpreter="perl"> vcfToolsStats.sh $filein $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog </command> <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> <param name="fileout_label" type="text" value="vcf_stats" optional="false" label="Output file basename"/> </inputs> <!-- [REQUIRED] Output files --> <outputs> <data name="fileout_annot" format="txt" label="${fileout_label}.annotation" /> <data name="fileout_het" format="txt" label="${fileout_label}.het" /> <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" /> <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" /> <data name="filelog" format="txt" label="${fileout_label}.log" /> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <param name="filein" value="sample.vcf" /> <output name="fileout_annot" file="stats-result.annotation" /> <output name="fileout_het" file="stats-result.het" /> <output name="fileout_imiss" file="stats-result.imiss" /> <output name="fileout_sum" file="stats-result.TsTv.summary" /> </test> </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> <help> .. class:: infomark **Authors** Adam Auton, Petr Danecek and Anthony Marcketta (C++ Module) : VCFtools_ .. _VCFtools: http://vcftools.sourceforge.net | **Please cite** "The Variant Call Format and VCFtools", Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, **Bioinformatics**, 2011 .. class:: infomark **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. .. class:: infomark **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr --------------------------------------------------- ================ VCF tools filter ================ ----------- Description ----------- | Compute statistics on VCF file | For further informations on VCFtools, please visite the VCFtools website_. .. _website: http://vcftools.sourceforge.net ----------------- Workflow position ----------------- **Upstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= **Downstream tools** =========== ========================== ======= Name output file(s) format =========== ========================== ======= =========== ========================== ======= ---------- Input file ---------- VCF file VCF file with all SNPs ---------- Parameters ---------- Output file basename Prefix for the output VCF file ------------ Output files ------------ .annotation file Statistics on annotation/location along genome .het file Statistics on heterozygosity of the individuals .imiss Statistics on missing data of the inidividuals .TsTv.summary Statistics on mutation types and transition/transvertion number .log file --------------------------------------------------- --------------- Working example --------------- Input files =========== VCF file --------- :: #fileformat=VCFv4.1 #FILTER=<ID=LowQual,Description="Low quality"> #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> [...] CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 Parameters ========== Output name -> vcf_stat Output files ============ .annotation file ---------------- :: Genic 4489 Intergenic 466 ======== Intron 960 Exon 3248 UTR 281 ======== Non-syn 226 Synonym 3022 .het file --------- :: INDV O(HOM) E(HOM) N_SITES F CATB1 0 0.0 3616 0.00000 .imiss file ----------- :: INDV N_DATA N_GENOTYPES_FILTERED N_MISS F_MISS CATB1 4813 0 0 0 .TsTv.summary file ------------------ :: MODEL COUNT AC 371 AG 1467 AT 562 CG 330 CT 1659 GT 397 Ts 3126 Tv 1660 </help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex"> @article{Danecek01082011, author = {Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis A. and Banks, Eric and DePristo, Mark A. and Handsaker, Robert E. and Lunter, Gerton and Marth, Gabor T. and Sherry, Stephen T. and McVean, Gilean and Durbin, Richard and 1000 Genomes Project Analysis Group}, title = {The variant call format and VCFtools}, volume = {27}, number = {15}, pages = {2156-2158}, year = {2011}, doi = {10.1093/bioinformatics/btr330}, abstract ={Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.Availability: http://vcftools.sourceforge.netContact: rd@sanger.ac.uk}, URL = {http://bioinformatics.oxfordjournals.org/content/27/15/2156.abstract}, eprint = {http://bioinformatics.oxfordjournals.org/content/27/15/2156.full.pdf+html}, journal = {Bioinformatics} } </citation> </citations> </tool>