Nonvariant Blocks Using END Key

Contiguous nonvariant segments of the genome can be represented as single records in gVCF. These records use the standard 'END' INFO key to indicate the extent of the record. Even though the record can span multiple bases, only the first base is provided in the REF field to reduce file size.

The following is a simplified segment of a gVCF file, describing a segment of nonvariant calls (starting with an A) on chromosome 1 from position 51845 to 51862.

##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

NA19238chr1 51845 . A . . PASS END=51862

Any field provided for a block of sites, such as read depth (using the DP key), shows the minimum value that is observed among all sites encompassed by the block. Each sample value shown for the block, such as the depth (DP), is restricted to a range where the maximum value is within 30% or 3 of the minimum. For example, for sample value range [x,y], y <= x+max(3,x*0.3). This range restriction applies to each of the sample values printed in the final block record.