Save Genotypes of unrelated Individuals

[TeaByrd]

Hello guys,

I'm asking how do I actually save the Genotypes of my simulation for unrelated Individuals? I don't know what to put into the 'fam' paramter of the writePED function. My code looks like this:

library(sim1000G)

# Read the example file included in sim1000G

vcf_file = file.path("MasterThesis/Aetionomy/AETIO_CS_postimpvcf_subset.vcf")
vcf = readVCF(vcf_file, min_maf = 0.02 , max_maf = NA)

vcf = readVCF( vcf_file, maxNumberOfVariants = 600 , min_maf = 0.01, max_maf = 1)

startSimulation(vcf, totalNumberOfIndividuals = 1000)
ids = generateUnrelatedIndividuals(200)

writePED(vcf, fam,filename = "Desktop/out_test_1000G") #what is my fam parameter in this case?

[adimitromanolakis]

Hi,

the fam parameter is a 6 column data matrix with the following columns: FamilyID, IndividualID, FatherID, MotherID, Gender, Status, Genotype Index for sim1000G. The first 6 columns correspond to the information that will be written in the PED file.

For your case you can use:

fam = data.frame( fid=ids, id=ids, dad=0,mom=0, gender=1, status=1, gtindex=ids )

Alternatively you can retrieve the genotypes with the function: retrieveGenotypes( ids[i] )

Best, Apostolos

On Wed, 28 Oct 2020 at 14:21, Thomas Lordick notifications@github.com wrote:

Hello guys,

I'm asking how do I actually save the Genotypes of my simulation for unrelated Individuals? I don't know what to put into the 'fam' paramter of the writePED function. My code looks like this:

library(sim1000G)

Read the example file included in sim1000G

vcf_file = file.path("MasterThesis/Aetionomy/AETIO_CS_postimpvcf_subset.vcf") vcf = readVCF(vcf_file, min_maf = 0.02 , max_maf = NA)

vcf = readVCF( vcf_file, maxNumberOfVariants = 600 , min_maf = 0.01, max_maf = 1)

startSimulation(vcf, totalNumberOfIndividuals = 1000) ids = generateUnrelatedIndividuals(200)

writePED(vcf, fam,filename = "Desktop/out_test_1000G") #what is my fam parameter in this case?

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[TeaByrd]

Thanks, Apolostos. The problem, I'm facing now is the following error when simulating:

[#.......] Reading VCF file..
Parsed with column specification:
cols(
  .default = col_character(),
  `#CHROM` = col_double(),
  POS = col_double()
)
See spec(...) for full column specifications.
[##......] Chromosome:   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22  Mbp:  0.041054  Region Size:  247529.8 kb  Num of individuals: 106 
[##......] Before filtering  Num of variants: 6815 Num of individuals: 106 
[###.....] After filtering  Num of variants: 6779 Num of individuals: 106 
[#####...] Creating SIM object
Warning: Some variants are not polymorphic. (n= 3179 )
[#####...] Haplodata object created
Error in startSimulation(vcf, totalNumberOfIndividuals = 1000) : Error: Genetic map does not match the region being simulated

Do I have to simulate chromosome-wise? Splitting the vcf file per chromosome and then simulate or what's the cause of the error in particular?

[adimitromanolakis]

Hi Thomas,

yes, it is only possible to simulate single chromosomes at the moment. We have not incorporated methods to correctly simulate whole genome data.

Best, Apostolos

On Fri, 30 Oct 2020 at 13:31, Thomas Lordick notifications@github.com wrote:

Thanks, Apolostos. The problem, I'm facing now is the following error when simulating:

[#.......] Reading VCF file.. Parsed with column specification: cols( .default = col_character(), #CHROM = col_double(), POS = col_double() ) See spec(...) for full column specifications. [##......] Chromosome: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Mbp: 0.041054 Region Size: 247529.8 kb Num of individuals: 106 [##......] Before filtering Num of variants: 6815 Num of individuals: 106 [###.....] After filtering Num of variants: 6779 Num of individuals: 106 [#####...] Creating SIM object Warning: Some variants are not polymorphic. (n= 3179 ) [#####...] Haplodata object created Error in startSimulation(vcf, totalNumberOfIndividuals = 1000) : Error: Genetic map does not match the region being simulated

Do I have to simulate chromosome-wise? Splitting the vcf file per chromosome and then simulate or what's the cause of the error in particular?

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[raqueldias]

Hi! On the same topic of saving the simulated genotypes of unrelated individuals: is there a way to save the genotypes in VCF format instead of PED?

[adimitromanolakis]

Hi Raquel,

no we haven't implemented such functionality yet in sim1000G but it would be a useful addition. You can try using plink to convert the ped file into a vcf.

Best, Apostolos

On Fri, 26 Feb 2021 at 02:38, Raquel Dias @.***> wrote:

Hi! On the same topic of saving the simulated genotypes of unrelated individuals: is there a way to save the genotypes in VCF format instead of PED?

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