Running OpenCRAVAT
OpenCRAVAT can be run via the Web Interface or Command line. Upon completion of an annotation run, results be viewed in the Interactive Viewer or by viewing the outputted files.
Input of multiple files
Submitting multiple input files is supported by OpenCRAVAT. The system will automatically merge and deduplicate your input files, and will only process each unique variant once. As a result, expected runtime for multiple input files depends on the uniqueness of the variants in each file. Runtimes will be the same as if each unique variant was submitted in a single file. OpenCRAVAT can process arbitrarily large numbers of input files. However, it may be hard to navigate the web viewer when more than 10 input files are used.
There are two input file formats currently supported by default: VCF and CRAVAT.
VCF Input Format
Variant Call Format (VCF) is a standard variant file format that is produced by sequencing centers and by variant calling software packages. A specification of the format is available here.
VCF files sometimes contain multiple variants on a single line (separated by commas in the ALT column). These variants can have different scores and annotations so the converter will split these into individual variants (e.g Reference base C Alternate base T and Reference base C Alternate base G).
Example
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##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=A,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 85729 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AD 0|0:48:1:51,51:0,1 1|0:48:8:51,51:4,4 1/1:43:5:.,.:1,4
20 1130053 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 1249593 . 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 1253923 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP:AD 0/1:35:4:2,2 0/2:17:5:2,3 1/1:40:3:2,1
22 30025797 TR1 A T 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ:AF 0|0:48:1:51,51:0 1|0:48:8:51,51:0.7 1/1:43:5:.,.:0.5
22 29050091 . A G 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|0:21:6:23,27 0|0:2:0:18,2 1/1:35:4
22 40418496 TR3 T C 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
22 40419252 . C T 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 1|0:54:7:56,60 0|1:48:4:51,51 0/0:61:2
12 122981745 TRI GGAAGAAGAA G,GGAA,GGAAGAA 50 PASS NS=3;DP=13;AA=T GT:GQ:HQ:AD 0|1:48:51,51:3,1 1|2:21:23,27:2,4 3|1:48:51,51:3,5
CRAVAT Input Format
OpenCRAVAT currently supports two input formats: CRAVAT format and VCF. The current version of OpenCRAVAT provides mappings and annotations based on the human genome reference sequence GRCh38. There is a feature in the OpenCRAVAT program to automatically convert hg18 or hg19 input files into GRCh38 coordinates.
The basic CRAVAT variant input file is a tab separated text file. Each row in a describes a genomic variant by the following sequential columns: Chromosome, Position, Strand, Reference-Base, Alternate-Base, [Sample], [Tags]. The table below describes each field:
Columns
Column |
Description |
Example |
|---|---|---|
Chromos ome |
The
chromosome,
prefixed
with
|
|
Positio n |
The numerical position of the nucleotide along the chromosome transcript. |
11250130 7, 1804372 |
Strand |
The strand
the variant
is on.
Either
|
|
Referen ce-Base |
The
reference
nucleotide,
or a |
|
Alterna te-Base |
The
alternate
nucleotide,
or |
|
Sample |
Optional: Sample identifier for cohort studies. |
|
Tags |
Optional: Arbitrary identifiers or category tags associated with the variant - delimited by semi-colon. |
|
Note if you wish to include tags but not sample ids, an extra tab character is needed between the alternate base and tag.
OpenCRAVAT processes a list of unique variants extracted from the input file. If the same variant is present in multiple samples, the variant will be presented as a single line in the results but the sample and mapping information can be used to identify all of the samples and original input lines associated with a line in the output.
Example
The following is a basic example of a CRAVAT input file:
chr2 112501307 + C A var001
chr14 104770363 + T A s1 var002
chrX 71127984 + A G s2 var003;control
chr14 91974629 + T G s1 var004;test
chr12 57094662 + G T s1 var005
The fields in the above sample must be tab delimited and may not get tabs if you copy / paste it.