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Kivvi VCF

Kivvi produces a VCF file for each region for each sample. The Kivvi VCF follows the standard VCF format specifications. The QUAL field contains a placeholder value. We have repurposed the sample column so that each column represents a completely assembled allele. In addition, we report the RU INFO field to represent the repeat units where a variant is found (repeat units are separated by comma). The four values for each repeat unit are:

  1. Repeat unit ID
  2. Where to find this repeat unit, represented as x.y, where x is the index of the allele and y is the index of the repeat unit on the allele.
  3. Read depth at this position for this repeat unit
  4. Number of reads supporting the variant

Example KIV2 VCF

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT allele1 allele2
chr6 160613775 . G C . PASS RU=31:2.3:31:31,30:2.4:30:30 GT 0 1

This variant is found on two repeat units:

  1. Repeat unit index #31, which is the third unit on the second allele (2.3). There are 31 reads covering this position for this repeat unit and 31 of those support the variant.
  2. Repeat unit index #30, which is the fourth unit on the second allele (2.4). There are 30 reads covering this position for this repeat unit and 30 of those support the variant.

This variant is only found on the second allele, so its GT is 0 for allele1 and 1 for allele2.

Example D4Z4 VCF

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT allele1 allele2 allele3
d4z4_ref 1611 . C G . PASS RU=73:2.3:19:19,44:2.6:21:21 GT 0 1 0

D4Z4 reference can be found here.