Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can resolve a wide range of different variant types with high accuracy. However, they require that all read alignments be available from the beginning of variant calling and be sorted by coordinates. Sorting is computationally expensive, both memory- and speed-wise, and the resulting pipelines suffer from storing and retrieving large alignments files from external memory. Therefore, there is interest in developing methods for resource-efficient variant calling.
Results: We present Ococo, the first program capable of inferring variants in a real-time, as read alignments are fed in. Ococo inputs unsorted alignments from a stream and infers single-nucleotide variants, together with a genomic consensus, using statistics stored in compact several-bit counters. Ococo provides a fast and memory-efficient alternative to the usual variant calling. It is particularly advantageous when reads are sequenced or mapped progressively, or when available computational resources are at a premium.
Brinda K, Boeva V, Kucherov G. Ococo: an online variant and consensus caller. arXiv:1712.01146 [q-bio.GN], 2018. https://arxiv.org/abs/1712.01146
Results from the paper were generated using code in the following repository: https://github.com/karel-brinda/ococo-paper-analysis. The entire computation is also available as a CodeOcean capsule.
git clone --recursive https://github.com/karel-brinda/ococo
cd ococo && make -j
./ococo -i test.bam -f test.fa --vcf-cons -conda install -c bioconda ococo
Prerequisities
- GCC 4.8+ or equivalent
- ZLib
Compilation: make
Installation: make install
SYNOPSIS
ococo -i <SAM/BAM file> [other options]
DESCRIPTION
Ococo is a program to call variants and a genomic consensus directly
from an unsorted SAM/BAM stream.
Input options:
-i, --input FILE
Input SAM/BAM file (- for standard input).
-f, --fasta-ref FILE
Initial FASTA reference (otherwise a seq of N's is used).
-s, --stats-in FILE
Input statistics.
Output options:
-F, --fasta-cons FILE Print consensus in FASTA.
-S, --stats-out FILE
Export statistics to a file.
-V, --vcf-cons FILE
Print inferred variants in VCF (- for standard output).
-P, --pileup FILE
Print SAMtools pileup (- for standard output).
--verbose
Use the verbose mode (report every update of a counter).
Parameters for consensus calling:
-x, --counters STR
Counter configuration [ococo32].
configuration bits/counter bits/position
ococo16 3 16
ococo32 7 32
ococo64 15 64
-m, --mode STR
Mode [batch].
mode description
real-time updates reported immediately
batch updates reported after end of algn stream
-q, --min-MQ INT
Skip alignments with mapping quality smaller than INT [1].
-Q, --min-BQ INT
Skip bases with base quality smaller than INT [13].
-w, --ref-weight INT
Initial counter value for nucleotides from ref [0].
-c, --min-cov INT
Minimum coverage required for update [2].
-M, --maj-thres FLOAT
Majority threshold [0.51].
Please use Github issues.
See Releases.