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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=<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
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