[Python] Do msprime simulated loci correspond with the actual positions using the input HapMap?

Discussão em 'Python' iniciado por Stack, Abril 20, 2025.

  1. Stack

    Stack Membro Participativo

    I am running msprime simulations using a legacy version (0.7.0) with the following call:

    recombination_map = msprime.RecombinationMap.read_hapmap(genetic_map_infile)

    sim = msprime.simulate(Ne = N_A,
    recombination_map = recombination_map,
    mutation_rate = mutation_rate,
    samples = samples,
    population_configurations = population_configurations,
    migration_matrix = migration_matrix,
    demographic_events = demographic_events,
    )


    Here's what the head of the hapmap file looks like:

    Chromosome Position(bp) Rate(cM/Mb) Map(cM)
    chr22 16050114 1.57022541745 0
    chr22 16057542 1.57022541745 0.0116636344008
    chr22 16058341 2.28516093455 0.0129182445094


    The output of this simulation is a VCF file that looks like:

    ##fileformat=VCFv4.2
    ##source=tskit 0.99.1
    ##FILTER=<ID=PASS,Description="All filters passed">
    ##contig=<ID=1,length=51241385>
    ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
    #CHROM POS ID REF ALT QUAL FILTER INFO ...
    1 3 . A T . PASS . GT 1|1 1|1 ...
    1 22 . A T . PASS . GT 0|0 0|0 ...
    1 27 . A T . PASS . GT 1|1 1|1 ...
    1 28 . A T . PASS . GT 0|0 0|0 ...
    ...
    1 51241382 . A T . PASS . GT 1|1 1|1


    It looks to me that the simulated VCF positions in the output correspond to the input chromosome positions in the hapmap, but I wanted to ask to be sure.

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