plink half missing call in .ped file
Then you can input your data, but you have to specify that you're missing FID, PID, ... /Programs/plink1.90/plink --file --ped plinkv2.raw --map plink.map --no-fid ... , Since VCF half calls are coded as "0/.", "./1",... PLINK/1.9 raises an error flag for such calls in the .ped file., (PLINK 1.9 has a --vcf-half-call flag which adjusts handling of VCF half-calls, but there are no plans to extend that functionality to .ped files.)., Possibly irregular .ped line. Restarting scan, assuming multichar alleles. Rescanning .ped file... 0% Error: Half-missing call in .ped file at variant ...,Hello, I am trying to analyse some genotyping data in PLINK. I started with the raw cluster *.idat files and converted them to PLINK workable files using GenomeStudio. ... Rescanning .ped file... 1% Error: Half-missing call in .ped file at variant 2, line,plink --file PolMEX --make-bed –snps rs10741657,rs3755967,rs3794060,rs3829251,rs4944957 ... Error: Half-missing call in .ped file at variant 219, line 1. , When I process this ped file in PLINK 1.9 to generate corresponding ... I get the following error: Error: Half-missing call in .ped file at variant 3, ..., '0' is normally the missing-genotype code. The body of a .ped line is supposed to look like “A C A A T G ...”.,These allow you to use .fam or .ped files which lack family ID, parental ID, sex, ... Missing genotype calls are normally assumed to be represented by '0' in .ped and .... 'haploid'/'h': Treat half-calls as haploid/homozygous (the , plink --tped chr1.tped --tfam subjects.tfam --recode --out chr1 ./plink --tped chr2.tped ... Error: Half-missing call in .ped file at variant 9, indiv 1.
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 plink half missing call in .ped file 相關參考資料
covert the file to .ped file - Biostars
Then you can input your data, but you have to specify that you're missing FID, PID, ... /Programs/plink1.90/plink --file --ped plinkv2.raw --map plink.map --no-fid ... https://www.biostars.org Dealing with half missing calls in ".ped" file - Biostars
Since VCF half calls are coded as "0/.", "./1",... PLINK/1.9 raises an error flag for such calls in the .ped file. https://www.biostars.org Error in converting data with half-missing genotypes - Google ...
(PLINK 1.9 has a --vcf-half-call flag which adjusts handling of VCF half-calls, but there are no plans to extend that functionality to .ped files.). https://groups.google.com Half missing call after going from illumina final report to plink ...
Possibly irregular .ped line. Restarting scan, assuming multichar alleles. Rescanning .ped file... 0% Error: Half-missing call in .ped file at variant ... https://groups.google.com Half missing genotype in *.ped files - Biostars
Hello, I am trying to analyse some genotyping data in PLINK. I started with the raw cluster *.idat files and converted them to PLINK workable files using GenomeStudio. ... Rescanning .ped file... 1% E... https://www.biostars.org How can I run a case-control study in Plink? - ResearchGate
plink --file PolMEX --make-bed –snps rs10741657,rs3755967,rs3794060,rs3829251,rs4944957 ... Error: Half-missing call in .ped file at variant 219, line 1. https://www.researchgate.net Matrix dosages to PED error - Google Groups
When I process this ped file in PLINK 1.9 to generate corresponding ... I get the following error: Error: Half-missing call in .ped file at variant 3, ... https://groups.google.com PLINK - error in --make-bed - Biostars
'0' is normally the missing-genotype code. The body of a .ped line is supposed to look like “A C A A T G ...”. https://www.biostars.org Standard data input - PLINK 1.9 - cog-genomics.org
These allow you to use .fam or .ped files which lack family ID, parental ID, sex, ... Missing genotype calls are normally assumed to be represented by '0' in .ped and .... 'haploid'/&#... https://www.cog-genomics.org Unwanted "zeros" when converting from tped+tfam to ped+ ...
plink --tped chr1.tped --tfam subjects.tfam --recode --out chr1 ./plink --tped chr2.tped ... Error: Half-missing call in .ped file at variant 9, indiv 1. https://groups.google.com |