VCF File Annotations

The locus is in region with conflicting indel calls. In any region where overlapping deletion evidence cannot be reolved into two haplotypes in the Germline mode, all indels and set records in the region are marked with the IndelConflict filter.

The site genotype conflicts with proximal indel call. For instance, a heterozygous SNV call made inside a heterozygous deletion.

The genotyping quality locus (GQX) is less than 30 or not present.

The fraction of base calls filtered out at a site is greater than the value 0.4. If many bases at the site are filtered out, it suggests that the site or position is bad.

The SNV strand bias value (SNVSB) exceeds 10.

The minimum of genotype quality assuming variant position and genotype quality assuming nonvariant position.

The genotype.

The genotype quality.

The filtered base call depth for site genotyping.

The base calls from input that are filtered before site genotyping.

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 versus all other intersecting indel alleles.

The SNV site strand bias.

The SNV homopolymer length.

The CIGAR alignment for each alternate indel allele

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.

The number of times RU is repeated in reference.

Number of times RU is repeated in indel allele.

End position of the region described in this record