Question

how to haplotyping from vcf file?how to analysis ld block?

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6.3 years ago

mmh7272 ▴ 60

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!

genome SNP gene • 1.8k views

ADD COMMENT • link updated 6.3 years ago by shubhra.bhattacharya ▴ 140 • written 6.3 years ago by mmh7272 ▴ 60

score 0 · Answer 1 · 2018-01-15

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6.3 years ago

shubhra.bhattacharya ▴ 140

Try Genotypevcf in GATK.

ADD COMMENT • link 6.3 years ago by shubhra.bhattacharya ▴ 140

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okay i try thank u for ur tip

ADD REPLY • link 6.3 years ago by mmh7272 ▴ 60

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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 REPLY • link 6.3 years ago by WouterDeCoster 47k

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

ADD REPLY • link 6.3 years ago by mmh7272 ▴ 60