How To Create Genome-Wide Estimation Of Ibd Sharing Using Plink From Tped Files?
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Entering edit mode
8.9 years ago
Kevin ▴ 640

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:
    --noweb
    --tfile chrY.vcf.gz.plinkformat
    --genome
    --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
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Entering edit mode

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?

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