VCF Format

Octopus reports variants in VCF 4.3 format.

Haplotypes

Octopus always reports phased genotypes (GT separated with | rather than /). The extent of phasing is provided in the PS FORMAT field, which refers to the POS of a previous record, so:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE

1 100 . A C . . . GT:PS 1|0:100

1 200 . G T . . . GT:PS 0|1:100

indicates the variants at positions 100 and 200 are phased. While

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE

1 100 . A C . . . GT:PS 1|0:100

1 200 . G T . . . GT:PS 0|1:200

indicates the variants are unphased. Note that phase sets may not be contiguous.

Spanning alleles

To represent complex multi-allelic loci, Octopus prefers a decompose alleles into multiple records and use the * allele to resolve conflicts. In particular, Octopus always splits variants that have unique REF alleles into multiple VCF records. For example, two overlapping deletions are represented like:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE

1 102738191 . ATTATTTAT A,* . . . GT 1|2

1 102738191 . ATTATTTATTTAT A,* . . . GT 2|1

In contrast, some other tools may choose to represent these variant with

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

1 102738191 . ATTATTTAT A . . . GT 1/0

1 102738191 . ATTATTTATTTAT A . . . GT 1/0

which is inconsistent as the reference is deduced in each record, or

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

1 102738191 . ATTATTTATTTAT ATTAT,A . . . GT 1/2

which is consistent, but rapidly becomes unmanageable as the length and number of overlapping variants increases.

Multiple * records

In some cases, a site may overlap with multiple distinct alleles. Octopus represents these sites using multiple * alleles in the ALT field.

Consider the realignments from the Ashkenazim trio:

The variants called by Octopus in this region are:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002 HG003 HG004

chr4 19232687 . A G 50 PASS AC=2;AN=6 GT:PS 0|1:19232687 0|0:19232687 0|1:19232687

chr4 19232728 . ATCTG A 50 PASS AC=2;AN=6 GT:PS:PQ 0|1:19232687 0|0:19232687 0|1:19232687

chr4 19232732 . GTCTGTCTATCTA G,*,* 50 PASS AC=2,2,2;AN=6 GT:PS 2|3:19232687 1|2:19232687 1|3:19232687

chr4 19232736 . G GTCTATCTA,* 50 PASS AC=2,2;AN=6 GT:PS 1|0:19232687 2|19232687 2|0:19232687

chr4 19232762 . C CTA 550 PASS AC=2;AN=6 GT:PS 0|1:19232687 0|0:19232687 0|1:19232687

chr4 19232762 . CTATATA C 50 PASS AC=2;AN=6 GT:PS 0|0:19232687 1|0:19232687 1|0:19232687

chr4 19232858 . A ACT 50 PASS AC=4;AN=6 GT:PS 0|1:19232687 1|0:19232687 1|1:19232687

Notably, Octopus reports two * alleles at the chr4:19232732 record. This indicates that there are two distinct alleles overlapping this site (at chr4:19232728 and chr4:19232736).

caution

In some rare cases, Octopus may report double * records in a single sample, resulting in calls like

1 100 . ACGT *,* 50 PASS AC=1,1;AN=2 GT 2|3

This generally indicates a homozygous deletion directly upstream of a heterozygous deletion, like:

1 99 . TA T 50 PASS AC=2;AN=2 GT:PS 1|1:99

1 100 . ACGT *,* 50 PASS AC=1,1;AN=2 GT:PS 2|3:99