VariantStore

VariantStore: A Large-Scale Genomic Variant Search Index

Overview

VariantStore is a system for efficiently indexing and querying genomic information (genomic variants and phasing information) from thousands of samples containing millions of variants. VariantStore builds a variant-oriented index by mapping each variant to the list of samples that contain the variant. Variants are indexed based on the positions where they occur. It supports querying variants occurring between two positions across a chromosome based on the reference or a sample coordinate. VariantStore can scale to tens of millions of variants and thousands of samples and can efficiently scale out-of-RAM to storage devices to enable memory-efficient construction and query.

API

• variantstore construct: construct a variation graph and position index.
• variantstore query: query variation graph for variants using the position index.
• variantstore draw: output a subgraph of the variation graph in the dot format.

Build

Library dependencies (given version or higher):

• g++ 7.5.0 (VariantStore needs C++17. C++17 features are available since GCC 5. Also tested on 7.3.0 but not other versions.)
• protobuf 3.7.1, C++ installation and trouble shooting, see here
• sdsl-lite
• zlib1g-dev 1:1.2.11.dfsg-0ubuntu2, or zlib-devel on CentOS
• libbz2-dev 1.0.6-8.1ubuntu0.2, or bzip2-devel on CentOS
• liblzma-dev 5.2.2-1.3, or xz-devel on CentOS
• gperftools-devel on CentO S

$ git clone https://github.com/Kingsford-Group/variantstore
$ cd variantstore
$ make proto
$ make variantstore

Construct variation graph

$ mkdir ser/ # make output folder
$ ./variantstore construct -r data/x.fa -v data/x.vcf.gz -p ser/

Expcted output

[2020-05-19 10:10:35.172] [info] Creating variant graph
[2020-05-19 10:10:35.208] [info] Building sample vector based variant graph.
[2020-05-19 10:10:35.208] [info] Adding mutations from: data/x.vcf.gz #Samples: 1
[2020-05-19 10:1u0:35.211] [info] Num mutations: 75 num mutations-sample: 75
[2020-05-19 10:10:35.211] [info] Num vars: 75
[2020-05-19 10:10:35.212] [info] Fixing sample indexes in the graph
[2020-05-19 10:10:35.212] [info] Graph stats:
[2020-05-19 10:10:35.212] [info] Chromosome: x #Vertices: 212 #Edges: 287 Seq length: 1074
[2020-05-19 10:10:35.212] [info] Serializing variant graph to disk
[2020-05-19 10:10:35.245] [info] Number of sample vector classes: 2
[2020-05-19 10:10:35.245] [info] Creating Index
[2020-05-19 10:10:35.246] [info] Serializing index to disk

The usage for this command are as follows:

SYNOPSIS
        variantstore construct -r <reference-file> -v <vcf-file> -p <output-prefix>

OPTIONS
        <reference-file>
                    reference file

        <vcf-file>  variant call format file

        <output-prefix>
                    output directory

Variant queries

$ ./variantstore query -p ser/ -t 6 -r 10:105 -m 0 -s 1 -o variant.txt -v

Expected output

[2020-05-19 10:19:08.284] [info] Loading Index ...
[2020-05-19 10:19:08.284] [info] Loading variant graph ...
[2020-05-19 10:19:08.284] [info] Read index only ..
[2020-05-19 10:19:08.329] [info] Graph stats:
[2020-05-19 10:19:08.329] [info] Chromosome: x #Vertices: 212 #Edges: 0 Seq length: 1074
[2020-05-19 10:19:08.329] [info] 6. Get variants in ref coordinate. 0
Number of variants get_var_in_ref: 8
Query1: (query_var_in_ref) Total Time Elapsed: 0.000426seconds

The usage for this command are as follows:

SYNOPSIS
        variantstore query -p <output-prefix> -t <query-type> -r <region> -m <mode> [-o <outfile>] [-s <sample-name>] [-a <alt-seq>] [-b <ref-seq>] [-v]

OPTIONS
        <output-prefix>
                    output directory

        <query-type>
                    Types of query.
                   1. Get sample's sequence in reference coordinates.
                   2. Get sample's sequence in sample coordinates.
                   3. Return closest variant in reference coordinates.
                   4. Get sample's variants in reference coordinates.
                   5. Get sample's variants in sample coordinates.
                   6. Get variants in reference coordinates.
                   7. Return samples with a given mutation.

        <region>    region in format <start>:<end>, regions separated by ','
        <mode>      READ_INDEX_ONLY: 0, READ_COMPLETE_GRAPH:1
        <outfile>   output_file

        <sample-name>
                    sample name

        <alt-seq>   alternative sequences, separated by ','
        <ref-seq>   reference sequences, separated by ','

        -v, --verbose
                    print vcf

Visualize variation graph

Output variation graph in the dot format

$ ./variantstore draw -p ser/ -r 10 -h 3

Visualize dot graph

$ make graph

Expected output

[2021-03-14 15:23:18.632] [info] Loading Index ...
[2021-03-14 15:23:18.632] [info] Loading variant graph ...
[2021-03-14 15:23:18.632] [info] Read complete graph ..
[2021-03-14 15:23:18.682] [info] Graph stats:
[2021-03-14 15:23:18.682] [info] Chromosome: x #Vertices: 212 #Edges: 0 Seq length: 1074
[2021-03-14 15:23:18.682] [info] Looking up vertex corresponding to the queried region

The usage for this command are as follows:

SYNOPSIS
        variantstore draw -p <output-prefix> -r <region> -h <hops> [-s <sample-name>] [-o <outfile>]

OPTIONS
        <output-prefix>
                    output directory

        <region>    region in format <start>:<end>, regions separated by ','
        <hops>      radius of the subgraph

        <sample-name>
                    sample name (default: REF)

Contributing

Contributions via GitHub pull requests are welcome.

Authors

• Prashant Pandey [email protected]
• Yinjie Gao [email protected]
• Carl Kingsford [email protected]