Analysis VCF entries

The VCF files for Analysis can have the following entries in the FILTER, FORMAT, and INFO fields:

Table: 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
OffTarget Variant is not on target

Table: 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: 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="">

Contribute to this article

Want to edit or suggest changes to this content? You can do so using GitHub.