Question: What if I break my VCF file into small VCF files and then generate Haplotype indivually and merge it for calculation of dn/ds calculation ?
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gravatar for Being Bioinformatician
3.0 years ago by
India
Being Bioinformatician160 wrote:

have VCf file which contain 1500 SNPs. Due to computational limitation , it is not possible for generating Haplotypes using PHASE program.

What if I break this VCF file into 5 separate VCF files and run the PHASE program individually and later on merging all the haplotype 2gether.

Is that a good idea or i just concentrate on SNPs which are present in the coding region of the genes.

Thanks in advance

vcf • 1.1k views
ADD COMMENTlink written 3.0 years ago by Being Bioinformatician160
1

Use another phasing program like beagle, fastPhase, mach, shapeit2, etc. They trivially work with 1500 SNPs. I would start from beagle or shapeit2.

ADD REPLYlink written 3.0 years ago by lh331k

Sir, I am trying to generate Haplotype file using beagle software using VCF file. But getting error. I have followed their tutorial but still stuck. even My .map file corresponding to VCF is returning error. Sir , Can you help me with small input files and command line . Thanks in advance

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Being Bioinformatician160
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