Question: how to haplotyping from vcf file?how to analysis ld block?
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gravatar for mmh7272
2.4 years ago by
mmh727250
mmh727250 wrote:

hi i am bioinformatics beginner i have a vcf file(this file include snp and positions by samples) how to haplotyping vcf file ? how to analysis ld block? i want see haploytyping group by phenotype data and draw ld block plz explain detaily thanks all!

snp gene genome • 957 views
ADD COMMENTlink modified 2.4 years ago by shubhra.bhattacharya120 • written 2.4 years ago by mmh727250
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gravatar for shubhra.bhattacharya
2.4 years ago by
shubhra.bhattacharya120 wrote:

Try Genotypevcf in GATK.

ADD COMMENTlink written 2.4 years ago by shubhra.bhattacharya120

okay i try thank u for ur tip

ADD REPLYlink written 2.4 years ago by mmh727250

Can you explain how that is going to help with creating haplotypes? As far as I know Genotype(g)vcf is used for calling variants.

ADD REPLYlink written 2.4 years ago by WouterDeCoster43k

thanks u for ur coment,Dr wounter de coster, Do u hava another tip about haplotype and ld block?

ADD REPLYlink written 2.4 years ago by mmh727250
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