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adimitromanolakis / sim1000G

Simulation of rare and common variants based on 1000 genomes data
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Genetic map does not match the region being simulated #10

Open zhangbs92 opened 2 years ago

zhangbs92 commented 2 years ago

Hi all, I am trying to simulate a family data by sim1000G. My genotype input is the UK Biobank genotype which is in binary files. Then I convert it to vcf file (not vcf.gz). Everything works fine except following error: genetic map does not match the region being simulated. In fact, I only use SNPs located in Chromosome 12, so I download the chromosome 12 map, but it just not working fine. Did anyone meet this before? How to fix this problem?

[#####...] Creating SIM object [#####...] Haplodata object created Error in startSimulation(vcf, totalNumberOfIndividuals = 10) : Error: Genetic map does not match the region being simulated Execution halted ERROR: read_short_data (id=a3b61a6d423baac5) returns an error. ERROR: [read_short_data]: [0]:

adimitromanolakis commented 2 years ago

Hi,

It is possible that there are some variants that do not overlap the genetic map, in the beginning or end of the chromosome. Please check the start and end locations of your vcf, if there are SNPs outside the extend of the genetic map. For example, the chromosome 12 genetic map spans from 148673 bp to 133778796 bp. Alternatively, you might be using another genome build, the genetic maps that are included in the package are for the GRCh37 build. Apostolos

On Wed, 21 Jul 2021 at 05:10, zhangbs92 @.***> wrote:

Hi all, I am trying to simulate a family data by sim1000G. My genotype input is the UK Biobank genotype which is in binary files. Then I convert it to vcf file (not vcf.gz). Everything works fine except following error: genetic map does not match the region being simulated. In fact, I only use SNPs located in Chromosome 12, so I download the chromosome 12 map, but it just not working fine. Did anyone meet this before? How to fix this problem?

[#####...] Creating SIM object [#####...] Haplodata object created Error in startSimulation(vcf, totalNumberOfIndividuals = 10) : Error: Genetic map does not match the region being simulated Execution halted ERROR: read_short_data (id=a3b61a6d423baac5) returns an error. ERROR: [read_short_data]: [0]:

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zhangbs92 commented 2 years ago

thank you so much, this is really helpful, the problem has been solved.