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GVM / Tools / Haplotype

HapView: is a haplotype analysis tool, calculating population specific frequencies for all haplotypes which observed from a list of query variants.

GVM Dataset
Custom Dataset

Species:

Populations:

Positions:

Chr Start End

Variation sites list

Using imputation data

yes no

Individual filter

Missing rate <= (range (0, 1), default 0.1)

Heterozy rate <= (range (0, 1), default 0.5)

Site filter

Missing rate <= (range (0, 1), default 0.1)

Minor allele frequency >= (range (0, 0.5), default 0.05)

Waiting for results...

Input vcf file

vcf file

Positions

Variation sites list

Regions

Is phased?

yes no

Only homozygous sites will be used for the calculation. If the user wants to use more sites to calculate haplotypes, it is recommended use phasing software to do the phase first.

Individual filter

Missing rate <= (range (0, 1), default 0.1)

Heterozy rate <= (range (0, 1), default 0.5)

Site filter

Missing rate <= (range (0, 1), default 0.1)

Minor allele frequency >= (range (0, 0.5), default 0.05)

Phenotype

yes no

Input genotype file

genotype file

Freq. in GVM

yes no

Species

Waiting for results...