Question: How To Create Genome-Wide Estimation Of Ibd Sharing Using Plink From Tped Files?
gravatar for Kevin
6.8 years ago by
Kevin610 wrote:

Hi! I am trying to do the below but using tped files generated from vcf tools

perform the genome-wide estimatation of IBD sharing:

plink --noweb --bfile nooutliers --genome --out nooutliersIBD

my command was

plink --noweb --tfile chrY.vcf.gz.plinkformat --genome --out chrY.vcf.gz.plinkformat.g

I had this error

Options in effect:
    --tfile chrY.vcf.gz.plinkformat
    --out chrY.vcf.gz.plinkformat.g

** For gPLINK compatibility, do not use '.' in --out **
Reading pedigree information from [ chrY.vcf.gz.plinkformat.tfam ] 
3000 individuals read from [ chrY.vcf.gz.plinkformat.tfam ] 
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 3000 missing
0 males, 0 females, and 3000 of unspecified sex
Warning, found 3000 individuals with ambiguous sex codes
These individuals will be set to missing ( or use --allow-no-sex )
Writing list of these individuals to [ chrY.vcf.gz.plinkformat.g.nosex ]
162 (of 162) markers to be included from [ chrY.vcf.gz.plinkformat.tped ]
Before frequency and genotyping pruning, there are 162 SNPs
Converting data to SNP-major format
3000 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 )
Converting data to Individual-major format
After frequency and genotyping pruning, there are 162 SNPs
After filtering, 0 cases, 0 controls and 3000 missing
After filtering, 0 males, 0 females, and 3000 of unspecified sex

 **Warning** this analysis typically requires whole-genome level data
             to give accurate results 

Writing whole genome IBS/IBD information to [ chrY.vcf.gz.plinkformat.g.genome ] 
Filtering output to include pairs with ( 0 <= PI-HAT <= 1 )
IBD(g) calculation: 0 of 6242811                  
ERROR: No nonmissing markers for individuals 0122 0122 - 0182 0182
plink • 3.9k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 6.8 years ago by Kevin610

As warning suggests 162 SNPs is not whole-genome level data. And error, I guess, is because 0122 0122 - 0182 0182 individuals has noCalls for all SNPs?

ADD REPLYlink written 5.3 years ago by zx87546.7k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1269 users visited in the last hour