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