OctopusCancer
The cancer calling model is for calling germline variation and somatic mutations in tumours. The model can jointly genotype multiple tumours from the same individual, and make use of a normal sample for improved classification power.
Usage: tumour-normal pairs#
To call germline and somatic mutations in a paired tumour-normal sample, just specify which sample is the normal (--normal-sample; -N):
It is also possible to genotype multiple tumours from the same individual jointly:
Usage: tumour only#
If a normal sample is not present the cancer calling model must be invoked explicitly:
Be aware that without a normal sample, somatic mutation classification power is significantly reduced.
VCF output#
By default both germline and somatic variants are called, somatic mutations are tagged with the SOMATIC INFO field. The GT fields for SOMATIC variants and any other variants in the same phase set (PS) are augmented with the number of unique somatic haplotypes inferred (somatic haplotypes are identified with the HSS tag). For example, in the following VCF:
The first phase set 1:50 includes a simple somatic mutation; it is not phased with any other variants. Downstream of this is another phase block starting at 1:100 that includes 2 germline and 2 somatic variants. The first somatic mutation in this phase set at 1:100 is phased onto the germline haplotype including the reference allele at the germline variant at 1:150. The second somatic mutation in this phase set is phased with the alternate allele of this germline variant. In the third phase set stating at 2:300 there is a somatic mutation that segregates with a germline variant at the same position, and another somatic mutation which is phased onto the same germline haplotype - the reference. The somatic allele in the multiallelic record is determined by looking at the HSS flags (1 indicates somatic), so "C>A" is the somatic mutation in this case. The third phase set starting at 3:100 includes 2 somatic mutations phased onto the same germline haplotype, but the first somatic mutation was inferred to segregate with both the germline allele and somatic allele at 3:150, suggests linear progression of the C>CC somatic mutation. The last phase set starting at 4:100 includes 2 somatic mutations phased onto the same germline haplotype, but not with each other.
QUAL vs PP#
For both paired and tumour-only calling, octopus reports two quality scores for each call (both germline and somatic):
QUALis the posterior probability the variant is segregating in the sample regardless of somatic classification.PP(anINFOfield) is the posterior probability the variant is segregating and classified correctly.
The difference between QUAL and PP indicates the uncertainty in the calls classification; a call may have high QUAL but low PP if the classification is uncertain (common in tumour-only calling or if the normal coverage is low). PP should always be less than QUAL in theory.
HPC, MAP_HF and HF_CR#
Octopus infers a probability distribution over haplotype frequencies, including any somatic haplotypes. For each variant in a phase-block with a SOMATIC variant, three statistics are reported that relate to haplotype frequency (per haplotype).
HPCis the Dirichlet posterior pseudo-count. Note that this count includes the prior count so should not be taken to mean the empirical count.MAP_HF(FORMAT) is the Maximum a Posteriori haplotype frequency point estimate.HF_CR(FORMAT) is a credible interval of the haplotypes frequency. The mass of the credible interval is specified by--credible-mass. The credible interval gives you an indication of how certain the MAP_HF estimate is; A very narrow interval means the MAP estimate is very certain, a wide interval means it is uncertain.
Performance considerations#
- The number of genotypes considered by the model
--max-genotypehas a significant impact on overall runtime. - The parameter
--max-somatic-haplotypescontrols the maximum number of unique segregating somatic haplotypes to be modelled. There must be at-least one somatic haplotype, but adding more can resolve somatic mutations falling on different germline haplotypes or multiple distinct haplotypes due to sub clonal evolution.
SOMATICs only#
To report only SOMATIC calls just add the --somatics-only command. This will only work if calls are beings filtered already (i.e. it will have no effect if -f off). It is generally not recommended to use this option until you are 100% satisfied with your calls, as call filtering will not work correctly if germline variants have been filtered from the VCF; you will not be able to re-filter your SOMATIC-only VCF.