error from ped file to bed file: Error: Half-missing call in .ped file at variant 2, line 50.

[LI LI]

Hi all, 

I have problem to run plink from "ped" file to "bed" file, there is an error Error: Half-missing call in .ped file at variant 2, line 50.

The files are here: https://www.dropbox.com/sh/bw6pfhh273iv0wl/AAB9sbnVNfonjpbnvzGdzK6ka?dl=0

PLINK v1.90b3.38 64-bit (7 Jun 2016)       https://www.cog-genomics.org/plink2

(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to /n/data1/hms/dbmi/avillach/autism-data/1Mv1_part1/1Mv1_part1.log.

Options in effect:

  --file /n/data1/hms/dbmi/avillach/autism-data/1Mv1_part1/1Mv1_part1

  --make-bed

  --out /n/data1/hms/dbmi/avillach/autism-data/1Mv1_part1/1Mv1_part1

96732 MB RAM detected; reserving 48366 MB for main workspace.

Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.

Rescanning .ped file... 49%

 

Error: Half-missing call in .ped file at variant 2, line 50.

Does anyone know how to solve this? Thanks.

[Christopher Chang]

How was the .ped file generated?  There is indeed a missing genotype at the beginning of line 50.

[Tania Quesada-Vargas]

I am running into the same problem.  If I use vcf to generate the bed file, then adding --vcf-half-call m (m is to change the half-calls for missing) does the trick, but if I generated the .ped file using vcftools, I don't know if there is an equivalent to indicate the program to change all half-calls as missing.

[Christopher Chang]

Usage of vcftools to generate .ped files was already obsolete 4 years ago.

[Farhad Farhadi]

Hi 

Sorry I have the same problem 

my SNPs are from dart seq and when I export (by dartR package) them as plink file, it gives me a binary format .csv I add 6 column mentioned in (http://zzz.bwh.harvard.edu/plink/data.shtml#ped) and then save it as tab delimited text file. make my map file following the above-mentioned link. when I try to read them  into plink ( ./plink --ped file.ped --map file.map), it gives the error: 

"Possibly irregular .ped line.  Restarting scan, assuming multichar alleles.

Rescanning .ped file... 0%

Error: Half-missing call in .ped file at variant 1, line 1."

I appreciate your help in this regard.

I use plink1.9 beta

  my ped file is like below

0 indiv1 0 0 0 0 -9 0 0 1 0 .............................

0 indiv2 0 0 0 0 -9 2 0 0 0 

[Christopher Chang]

You have “-9” phenotype values in the 7th column; those are supposed to be in the 6th column.

[Farhad Farhadi]

no it is not for phenotype value(I have put ). it has been on my file created by dartfile. seems to be missing data.

[Farhad Farhadi]

I have put 0 as phenotype value since I dont have.