EMBOSS: variationget

| 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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-variation] (Parameter 1) | variation | Variation filename and optional format, or reference (input query) | Variation entries |
[-outfile] (Parameter 2) | outvariation | (no help text) outvariation value | Variation entries |
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-variation" associated variation qualifiers
-iformat1 -iformat_variation | string | Input variation format | Any string |
-iquery1 -iquery_variation | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_variation | integer | Input start position offset | Any integer value | 0
-idbname1 -idbname_variation | string | User-provided database name | Any string |
"-outfile" associated outvariation qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | Any string |
-oformat2 -oformat_outfile | string | Variation output format | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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 called 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|0:10,10	0|0:10,10	0/1:3,3
    19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	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;AN=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 called 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|0:10,10	0|0:10,10	0/1:3,3
    19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	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;AN=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 © 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