Skip to content

Latest commit

 

History

History
118 lines (87 loc) · 3.16 KB

define.md

File metadata and controls

118 lines (87 loc) · 3.16 KB
Raw

Defining a Graph

Updated: May 11, 2017

vargas define --help

Define subgraphs deriving from a reference and VCF file.
Usage:
  vargas define [OPTION...]

 Required options:
  -f, --fasta arg  <str> *Reference FASTA filename.

 Optional options:
  -v, --vcf arg       <str> Variant file (vcf, vcf.gz, or bcf).
  -t, --out arg       <str> Output filename. (default: stdout)
  -g, --region arg    <CHR[:MIN-MAX];...> CSV list of regions. (default: all)
  -s, --subgraph arg  <str> Subgraph definitions, see below.
  -p, --filter arg    <str> Filter by sample names in file.

  -h, --help  Display this message.

In the simplest form, a linear graph can be defined with just a FASTA file. The graph can be constrained to certain regions:

vargas define -f GRCh38.fa -g "chr1;chr2;chr3:0-10,000,000;chr4"

Adding a VCF file will include variants into the graph. Variants can be restricted to certain samples using --filter.

Subgraphs

A Hierarchy of graphs can be defined and alignments targeted at specific subgraphs. The graph with all of the variants is the base graph. ref refers to the linear graph only consisting of reference nodes, and maxaf picks the nodes with the highest allele frequency.

Subgraphs are defined using the format label=N[%], where N is the number of samples or percentage of samples to select. The samples are selected from the parent graph, scoped with ':'. For example : a=50;a:b=20%;a:c=5. The 5 samples in a:c will all be in a. Likewise, The 10 samples in a:b will also be in a.

Example

multigraph.vcf :

##fileformat=VCFv4.0
##contig=<ID=chrA>
##contig=<ID=chrB>
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  SA  SB
chrA    40  rs775809821 A   T,C .   .   AF=0.5  GT  1|0 2|0
chrA    41  rs768019142 A   TA,G    .   .   AF=0.2,0.3  GT  2|1 0|0
chrA    60  rs62651026  A   T,A .   .   AF=0.1,0.2  GT  0|2 1|0
chrB    40  rs376007522 C   T,G .   .   AF=0.8,0.1  GT  0|2 0|1
chrB    80  rs796688738 C   AC,<CN0>    .   .   AF=0.05,0.1 GT  2|1 1|1

multigraph.fa :

>chrA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>chrB
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

Defining with the defintion "a=3;a:b=2;a:b:c=1" will generate the base, maxaf, ref, a, a:b, and a:b:c graphs.

vargas define -f ref.fa -v ref.vcf -t ref.gdef -s "a=3;a:b=2;a:b:c=1"

Converting to DOT format:

vargas query -d multigraph.gdef -d <graphname> -t <graphname>.dot

Base graph

Base Graph

a:b graph

ab

Max allele frequency graph

maxaf

File format

 @vgraph
 date <graph build date>
 fasta <reference fasta name>
 vargas-build <vargas build date>
 vcf <vcf file name>
 [other meta info]

 @contigs
 <offset> <contig name>
 ...

 @graphs
 <name> <node id list> <edges>
 ...

 @nodes
 <ID> <endpos> <frequency> <pinched> <ref> <seqsize>
 <node sequence>
 ...