Isaac Whole Genome Sequencing VCF Entries

The VCF files for Isaac Whole Genome Sequencing can have the following entries in the FILTER, FORMAT, and INFO fields:

Table 2 VCF FILTER Entries
Entry	Description
IndelConflict	Locus is in region with conflicting indel calls
SiteConflict	Site genotype conflicts with proximal indel call, typically a heterozygous SNV call made inside of a heterozygous deletion
LowGQX	Locus GQX is less than 30 or not present
HighDPFRatio	The fraction of base calls filtered out at a site is greater than 0.4
HighSNVSB	SNV strand bias value (SNVSB) exceeds 10
HighDepth	Locus depth is greater than 3x the mean chromosome depth

Table 3 VCF FORMAT Entries
Entry	Description
GQX	Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}
GT	Genotype
GQ	Genotype Quality
DP	Filtered base call depth used for site genotyping
DPF	Base calls filtered from input before site genotyping
AD	Allelic depths for the ref and alt alleles in the order listed. For indels, this value only includes reads that confidently support each allele (posterior probability 0.999 or higher that read contains indicated allele vs all other intersecting indel alleles)
DPI	Read depth associated with indel, taken from the position preceding the indel.

Table 4 VCF INFO Entries
Entry	Description
SNVSB	SNV site strand bias
SNVHPOL	SNV contextual homopolymer length
CIGAR	CIGAR alignment for each alternate indel allele
RU	Smallest repeating sequence unit extended or contracted in the indel allele relative to the reference. RUs longer than 20 bases are not reported.
REFREP	Number of times RU is repeated in reference.
IDREP	Number of times RU is repeated in indel allele.
END	End position of the region described in this record
BLOCKAVG_min30p3a	Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block


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