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GVM
/
Tools
/ Haplotype
Haplotype tool
Calculate population specific haplotype frequencies of all haplotypes observed for a list of query variants.
GVM Dataset
Custom Dataset
Species:
Animals-----------
Felis catus(cat Felis_catus_9.0)
Bos taurus(cattle UMD_3.1)
Gallus gallus (chicken Gallus_gallus5.0)
Ailuropoda melanoleuca (giant panda ASM200744v2)
Capra hircus (goat CHIR_2.0)
Homo sapiens (human GRCh37)
Equus ferus (horse EquCab2.0)
Sus scrofa (pig Sscrofa10.2)
Ovis aries (sheep Oar_v4.0)
Equus caballus (tarpan EquCab2.0)
Plants-----------
Cannabis sativa (cannabis GCF_900626175.1)
Manihot esculenta (cassava Manihot_esculenta6.1)
Gossypium hirsutum (cotton Ghir.BGI)
Phaseolus vulgaris (common bean Pvulgaris_442_v2.0)
Brassica rapa (field mustard CAAS_Brap_v3.01)
Vitis vinifera (grape IGGP 12x)
Zea mays (maize RefGen_v4)
Populus trichocarpa (poplar JGI v3.0)
Oryza sativa (rice IRGSP1.0)
Sorghum bicolor (sorghum Sbiv3.1)
Glycine max (soybean Wm82.a2.v1)
Solanum lycopersicum (tomato SL2.50)
Populations:
Positions:
Chr
Chr01
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
Animals-----------
Sus scrofa (pig Sscrofa10.2)
Plants-----------
Zea mays (maize RefGen_v4)
Oryza sativa (rice IRGSP1.0)
Sorghum bicolor (sorghum Sbiv3.1)
Glycine max (soybean Wm82.a2.v1)
Waiting for results...
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