Introduction

Octopus calls variants and genotypes using a Bayesian model. Like any model, there are some aspects of real error that are not fully captured in the model which can lead to false calls. We therefore recommended filtering calls to improve precision.

There are currently two approaches available in Octopus for filtering variants:

1. Hard coded thresholds
2. Random forests

Both methods use annotations computed by Octopus.

The random forest approach is preferred when sufficient training data is available (e.g. typical germline and somatic calling). Hard coded thresholds are appropriate for other cases (e.g. UMI low frequency calling).

Annotations

Octopus provides various annotations for filtering variants. To list available annotations, use the command

$ octopus --help --annotations

For example, the current annotations are:

Name Kind Number Type Description

AC FORMAT A Integer "Number of non-reference alleles called for each sample"

AD FORMAT R Integer "Empirical allele depth"

ADP FORMAT 1 Integer "Number of reads overlapping the position that could be assigned to an allele"

AF FORMAT R Float "Empirical allele frequency (AD / ADP)"

AFB FORMAT R Float "Absolute difference between empirical allele frequency (AF) and expected allele frequency given genotype"

AMQ FORMAT R Integer "Median mapping quality of reads assigned to each allele"

ARF FORMAT 1 Float "Fraction of reads overlapping the call that cannot be assigned to a unique haplotype"

BMC FORMAT 1 Integer "Number of base mismatches at variant position in reads supporting variant haplotype"

BMF FORMAT 1 Float "Fraction of base mismatches at variant position"

BMQ FORMAT 1 Integer "Median quality of base mismatches in reads assigned to a unique allele"

BQ FORMAT R Integer "Median base quality of reads supporting each allele"

CC INFO 1 Float "PP divided by QUAL"

CRF INFO 1 Float "Fraction of clipped reads covering the call"

DAD FORMAT R Integer "Number of realigned reads supporting ALT alleles identified as duplicates"

DAF FORMAT R Float "Fraction of realigned reads supporting ALT alleles identified as duplicates"

DC INFO 1 Float "Number of reads supporting a de novo haplotype in the normal"

DENOVO FORMAT 1 Integer "DENOVO status of each sample"

DP FORMAT 1 Integer "Number of read overlapping the call"

DPC FORMAT 1 Float "Concordance of allele support from duplicate reads"

ER FORMAT R Float "Error rate in supporting reads"

ERS FORMAT R Float "Error rate standard deviation in supporting reads"

FRF FORMAT 1 Float "Fraction of reads filtered for calling"

GC INFO 1 Float "GC bias of the reference in a window centred on the call"

GQ INFO A Integer "Number of non-reference alleles called for each sample"

GQD FORMAT 1 Float "GQ divided by DP"

ITV INFO A Flag "Is the variant a transversion"

MC FORMAT 1 Integer "Number of mismatches at variant position in reads supporting variant haplotype"

MF FORMAT 1 Float "Fraction of reads with mismatches at variant position"

MHL FORMAT . Integer "Mean likelihood (Phreds) of reads overlapping the site assigned to each haplotype"

MP INFO 1 Float "Model posterior for this haplotype block"

MQ INFO 1 Float "Mean mapping quality of reads overlapping the call"

MQ0 INFO 1 Integer "Number of reads overlapping the call with mapping quality zero"

MQD FORMAT 1 Integer "Maximum pairwise difference in median mapping qualities of reads supporting each haplotype"

MRC FORMAT 1 Integer "Number of reads supporting the call that appear misaligned"

MRL FORMAT 1 Integer "Maximum read length overlapping the site"

NC INFO 1 Float "Fraction of overlapping reads supporting a somatic haplotype in the normal"

PLN FORMAT 1 Integer "Length of the phase block for the call"

PP INFO 1 Float "Call posterior probability"

PPD INFO 1 Float "PP divided by DP"

QD INFO 1 Float "QUAL divided by DP"

QUAL INFO A Integer "Number of non-reference alleles called for each sample"

REB FORMAT 1 Float "Probability allele occurs at the end (head or tail) of supporting reads"

REFCALL FORMAT 1 Integer "REFCALL status of each sample"

RSB FORMAT 1 Float "Bias of variant side (head or tail half) in supporting reads"

RTB FORMAT 1 Float "Probability allele occurs in the tail of supporting reads"

SB FORMAT 1 Float "Strand bias of reads based on haplotype support"

SD FORMAT 1 Float "Strand bias of reads overlapping the site; probability mass in tails of Beta distribution"

SF FORMAT 1 Float "Max fraction of reads supporting ALT alleles that are supplementary"

SHC FORMAT 1 Integer "Number of called somatic haplotypes"

SMQ FORMAT 1 Integer "Median mapping quality of reads assigned to called somatic haplotypes"

SOMATIC FORMAT 1 Integer "SOMATIC status of each sample"

STRL INFO 1 Integer "Length of overlapping STR"

STRP INFO 1 Integer "Period of overlapping STR"

VL FORMAT 1 Integer "Maximum length of called alleles"