                                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:6.5.6.0

   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=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in call
ed genotypes">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for
each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=CNV,Description="Copy number variable region">
#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,<DEL:ME:ALU>  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=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in call
ed genotypes">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for
each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=CNV,Description="Copy number variable region">
#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,<DEL:ME:ALU>  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
