« Previous - Version 2/3 (diff) - Next » - Current version
Marta Bleda, 05/18/2012 10:11 pm


Input formats

< Back to the Main page

VARIANT input formats

Currently, the supported input formats in VARIANT are:

VCF 4.0

VARIANT supports the VCF4 format from 1000 genomes project, a detailed description can be found at:

http://www.1000genomes.org/node/101

Here you can find an example of the format (taken form 1000 genoem project):

##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=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">
#CHROM POS     ID        REF ALT    QUAL FILTER INFO                              FORMAT      NA00001        NA00002        NA00003
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|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20     1234567 microsat1 GTCT   G,GTACT 50   PASS   NS=3;DP=9;AA=G                    GT:GQ:DP    0/1:35:4       0/2:17:2       1/1:40:3

VCF 4.1

We are working in new VCF4.1 format, currently is a draft but we will support it soon:

http://www.1000genomes.org/wiki/Analysis/variant-call-format

VCF4.1 format features can be found at:

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

GFF2

GFF2 specifications can be found at http://www.sanger.ac.uk/resources/software/gff/spec.html.

Example (from Sanger web site):

SEQ1  EMBL  atg  103  105  .  +  0
SEQ1  EMBL  exon  103  172  .  +  0
SEQ1  EMBL  splice5  172  173  .  +  .
SEQ1  netgene  splice5  172  173  0.94  +  .
SEQ1  genie  sp5-20  163  182  2.3  +  .
SEQ1  genie  sp5-10  168  177  2.1  +  .
SEQ2  grail  ATG  17  19  2.1  -  0

BED

BED specifications can be found at http://genome.ucsc.edu/FAQ/FAQformat#format1

Example (from UCSC web site):

chr7    127471196    127472363    Pos1    0    +    127471196    127472363    255,0,0
chr7    127472363    127473530    Pos2    0    +    127472363    127473530    255,0,0
chr7    127473530    127474697    Pos3    0    +    127473530    127474697    255,0,0
chr7    127474697    127475864    Pos4    0    +    127474697    127475864    255,0,0
chr7    127475864    127477031    Neg1    0    -    127475864    127477031    0,0,255
chr7    127477031    127478198    Neg2    0    -    127477031    127478198    0,0,255
chr7    127478198    127479365    Neg3    0    -    127478198    127479365    0,0,255
chr7    127479365    127480532    Pos5    0    +    127479365    127480532    255,0,0
chr7    127480532    127481699    Neg4    0    -    127480532    127481699    0,0,255