The locus is in region with conflicting indel calls.
SiteConflict
The site genotype conflicts with proximal indel call. For instance, a heterozygous SNV call made inside a heterozygous deletion.
LowGQX
The genotyping quality locus (GQX) is less than 30 or not present.
HighDPFRatio
The fraction of base calls filtered out at a site is greater than the value 0.4.
HighSNVSB
The SNV strand bias value (SNVSB) exceeds 10.
OffTarget
The variant is not on target.
Table 31 FORMAT Heading Table
Annotation
Description
GQX
The minimum of genotype quality assuming variant position and genotype quality assuming non-variant position.
GT
The genotype name.
GQ
The genotype quality.
DP
The filtered base call depth for site genotyping.
DPF
The base calls from input that are filtered before site genotyping.
AD
The allelic depths for the reference and alternate alleles in the order that are listed.
For indels, the value includes reads that support each allele. The posterior probability value of 0.999 or higher read contains indicated allele verses all other intersecting indel alleles.
DPI
The read depth associated with indel, taken from the position preceding the indel.
Table 32 INFO Heading Table
Annotation
Description
SNVSB
The SNV site strand bias.
SNVHPOL
The SNV homopolymer length.
CIGAR
The CIGAR alignment for each alternate indel allele
RU
The smallest repeating sequence unit extended or contracted in the indel allele relative to the reference. RUs that are longer than 20 bases are not reported.
REFREP
The 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
The non-variant site block. All sites in a block are non-variant.
The sites have the same filter value and have 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.