Ploidy Caller Output File

The Ploidy Caller generates a <output-file-prefix>.ploidy.vcf.gz output file in the output directory. The output file follows the VCF 4.2 Specification. A single record is reported for each reference autosome and allosome, except for the Y chromosome if the reference sex karotype is XX. Calls are not made for other sequences in the reference genome, such as mitochondrial DNA, unlocalized or unplaced sequences, alternate contigs, decoy contigs, or the Epstein-Barr virus sequence.

The following information is provided in the VCF file.

•

Meta information—The VCF output file contains common meta-information such as DRAGENVersion and DRAGEN CommandLine, as well as Ploidy Caller specific information. The VCF header contains the meta-information for median autosome depth of coverage, the provided sex karyotype if available, the estimated sex karyotype from the Ploidy Estimator if available, and the reference sex karyotype. The following is an example of the header lines:

•

FILTER fields—The VCF output file includes the LowQual filter, which filters results with quality score below 20.

•

INFO Fields—The VCF output INFO fields include the following:

–

END—End position of the variant described in this record.

–

SVTYPE—Type of structural variant.

•

Format fields—The VCF output file includes the following format fields. There is no GT FORMAT field. A variant call in the VCF displays either <DUP> or <DEL> in the ALT column. A non-variant call displays . in the ALT column. If using the output file for downstream use, a GT field can be added for variant calls using ./1 for a diploid contig and 1 for a haploid contig. For non-variant calls, use 0/0 for diploid and 0 for haploid.

–

DC—Depth of coverage.

–

NDC—Normalized depth of coverage.

The following is an example output file.

 

##fileformat=VCFv4.2

...

##autosomeDepthOfCoverage=36.635

##providedSexKaryotype=XY

##estimatedSexKaryotype=X0

##referenceSexKaryotype=XY

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

##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">

##ALT=<ID=DEL,Description="Deletion relative to the reference">

##ALT=<ID=DUP,Description="Region of elevated copy number relative to the reference">

##FILTER=<ID=LowQual,Description="QUAL below 20">

##FORMAT=<ID=DC,Number=1,Type=Float,Description="Depth of coverage">

##FORMAT=<ID=NDC,Number=1,Type=Float,Description="Normalized depth of coverage">

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MySampleName

chr1 1 . N . 31.1252 PASS END=248956422 DC:NDC 36.836:1.00549

chr2 1 . N . 31.451 PASS END=242193529 DC:NDC 36.668:1.0009

...

chr21 1 . N . 31.4499 PASS END=46709983 DC:NDC 36.6:0.999045

chr22 1 . N . 28.8148 PASS END=50818468 DC:NDC 37.2:1.01542

chrX 1 . N . 29.7892 PASS END=156040895 DC:NDC 18:0.982667

chrY 1 . N <DEL> 150 PASS END=57227415;SVTYPE=DEL DC:NDC 5.7:0.311178

```