Question: ROH by PLINK
1
gravatar for afadda
4.0 years ago by
afadda10
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afadda10 wrote:

Hi,

I'm running the following command to find runs of homozygosity: 

plink --bfile path/G02 --homozyg --out path/G02 --allow-no-sex

I get this log:

Writing this text to log file [ path/G02.log ]

Analysis started: Sun May  3 14:16:01 2015


Options in effect:

    --bfile path/G02

    --homozyg

    --out path/G02

    --allow-no-sex


Reading map (extended format) from [path/G02.bim ] 

3923914 markers to be included from [ path/G02.bim ]

Reading pedigree information from [ path/G02.fam ] 

1 individuals read from [ path/G02.fam ] 

0 individuals with nonmissing phenotypes

Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)

Missing phenotype value is also -9

0 cases, 0 controls and 1 missing

0 males, 0 females, and 1 of unspecified sex

Warning, found 1 individuals with ambiguous sex codes

Writing list of these individuals to [ path/G02.nosex ]

Reading genotype bitfile from [ path/G02.bed ] 

Detected that binary PED file is v1.00 SNP-major mode

Before frequency and genotyping pruning, there are 3923914 SNPs

1 founders and 0 non-founders found

Total genotyping rate in remaining individuals is nan

0 SNPs failed missingness test ( GENO > 1 )

0 SNPs failed frequency test ( MAF < 0 )

After frequency and genotyping pruning, there are 3923914 SNPs

After filtering, 0 cases, 0 controls and 1 missing

After filtering, 0 males, 0 females, and 1 of unspecified sex

Converting data to Individual-major format


Writing homozygosity-run information to [ path/G02.hom ] 

Run defined as: 

Homozygous segment criteria:

  length (kb)       = 1000

  # SNPs (N)        = 100

  density (kb/SNP)  = 50

  largest gap (kb)  = 1000

1 of 1 individuals      


Writing segment summary to [path/G02.hom.indiv ]

Writing segment summary to [ path/G02.hom.summary ]

I get nothing in the homo files except the headings. Anyone has any idea on why this is?

 

thanks!

plink roh • 3.7k views
ADD COMMENTlink modified 3.8 years ago by Biostar ♦♦ 20 • written 4.0 years ago by afadda10

In .ped file, if you don't have information for family ID, paternal, maternal and sex ID, then specified "0" instead -9. It would solve your problem.

 

ADD REPLYlink written 4.0 years ago by kumar.vinod81280
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