CODEWITHSUNDEEP
pythonbioinformaticsgenomegenomics
rbierman
rbierman

Reputation: 91

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

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.

Upvotes: 0

Views: 34

Answers (0)

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