variationget Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Get sequence variations Description variationget reads sequence variation data and writes the data in one of the EMBOSS variation output formats. Usage Here is a sample session with variationget % variationget valid-4.0.vcf Get sequence variations Variation output file [0.vcf]: test.vcf Go to the input files for this example Go to the output files for this example Command line arguments Get sequence variations Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-variation] variation Variation filename and optional format, or reference (input query) [-outfile] outvariation (no help text) outvariation value Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-variation" associated qualifiers -iformat1 string Input variation format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -idbname1 string User-provided database name "-outfile" associated qualifiers -odirectory2 string Output directory -oformat2 string Variation output format General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format variationget reads sequence variation data. Input files for usage example File: valid-4.0.vcf ##fileformat=VCFv4.0 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##ALT= ##ALT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 19 111 . A C 9.6 . . GT:HQ 0|0:10,1 0 0|0:10,10 0/1:3,3 19 112 . A G 10 . . GT:HQ 0|0:10,1 0 0|0:10,10 0/1:3,3 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0. 5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0. 333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 :.,. 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP :HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. 20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;A N=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 20 1235237 . T . . . . GT 0/0 0|0 ./. X 9 . A T 12.1 . . GT 0 0/1 1/0 X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 X 11 rsTest2 T A, 10 q10;s50 . GT:DP:GQ .:3:10 ./. 0|2:3 X 12 . T A 13 . . GT 0 1/0 1/1 Output file format Output files for usage example File: test.vcf ##fileformat=VCFv4.0 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FILTER= ##FILTER= ##ALT= ##ALT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 19 111 . A C 9.6 . . GT:HQ 0|0:10,1 0 0|0:10,10 0/1:3,3 19 112 . A G 10 . . GT:HQ 0|0:10,1 0 0|0:10,10 0/1:3,3 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0. 5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0. 333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 :.,. 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP :HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. 20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;A N=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 20 1235237 . T . . . . GT 0/0 0|0 ./. X 9 . A T 12.1 . . GT 0 0/1 1/0 X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 X 11 rsTest2 T A, 10 q10;s50 . GT:DP:GQ .:3:10 ./. 0|2:3 X 12 . T A 13 . . GT 0 1/0 1/1 Data files None. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description abiview Display the trace in an ABI sequencer file coderet Extract CDS, mRNA and translations from feature tables entret Retrieve sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment infoalign Display basic information about a multiple sequence alignment infoseq Display basic information about sequences refseqget Get reference sequence seqxref Retrieve all database cross-references for a sequence entry seqxrefget Retrieve all cross-referenced data for a sequence entry showalign Display a multiple sequence alignment in pretty format whichdb Search all sequence databases for an entry and retrieve it Author(s) Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None