FileIndexChrPos |
Index a file that has "chr \t pos" as the beginning of a line (e.g.
|
LineChrPos |
A simple chr:pos parser
Stores using bytes instead of chars
|
Pedigree |
A pedigree for cancer samples
|
PedigreeEntry |
Pedigree entry in a VCF file header
E.g.:
##PEDIGREE=
or
##PEDIGREE=
|
VariantVcfEntry |
Variant + VcfEntry
This is used to 'outer-join' a VcfEntry into all its constituent variants.
|
VcfConsequence |
An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP)
Format:
##INFO=
|
VcfConsequenceHeader |
An 'CSQ' entry in a vcf header line
|
VcfEffect |
An 'ANN' or 'EFF' entry in a VCF INFO field
Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12)
*
|
VcfEntry |
A VCF entry (a line) in a VCF file
|
VcfGenotype |
A VCF genotype field
There is one genotype per sample in each VCF entry
|
VcfHeader |
Represents the header of a vcf file.
|
VcfHeaderEntry |
Represents a info elements in a VCF file's header
References:
https://samtools.github.io/hts-specs/VCFv4.3.pdf
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
|
VcfHeaderFormat |
|
VcfHeaderInfo |
Represents a info elements in a VCF file
References: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
INFO fields should be described as follows (all keys are required):
##INFO=
Possible Types for INFO fields are: Integer, Float, Flag, Character, and String.
|
VcfLof |
An 'LOF' entry in a vcf line
|
VcfNmd |
An 'NMD' entry in a vcf line
|