Octopus Variants Track Settings

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Variants Identified by Octopus (All Variation and Repeats tracks)

Display mode:

Filters

Exclude variants with Quality/confidence score (QUAL) score less than
Exclude variants with these FILTER values:

	PASS (All filters passed)
	ADP (Assigned depth is low)
	DP (Read depth around variant is low)
	LBQ (Median base quality supporting variant is low)
	SB (One of the alternative alleles has strand bias)
	AFB (The called allele frequencies are not as expected for the given ploidy)
	AF (The emperical allele frequency is low)
	AD (Low empirical allele depth)
	MP (Variant failed model posterior filter)
	MQ (Mapping quality across calling region is low)
	q10 (Variant quality is below 10)

Minimum minor allele frequency (if INFO column includes AF or AC+AN):

VCF configuration help

View table schema

Data last updated at UCSC: 2022-10-20

Description

This track shows the sequence variants identified by Octopus. The D. kikkawai genomic Illumina dataset used in this analysis was obtained from the NCBI Sequence Read Archive under the accession number SRR345537.

References

Cooke DP, Wedge DC, Lunter G. A unified haplotype-based method for accurate and comprehensive variant calling. Nat Biotechnol. 2021 Jul;39(7):885-892. doi: 10.1038/s41587-021-00861-3.