samples in vcf not in ped

[Giuseppe1995]

Hi,
I'm trying to run peddy on a set of 339 samples whose variants have been jointly called.
first, from the VCF, I used plink to convert it (let's call it $VCF) to ped/map format using plink (generating a respective $PED file).
very simply, I subsequently run the command specified here:

peddy --plot -p 4 --prefix mystudy $VCF $PED

but, although I receive no errors, it gives me back the following warning:

"WARNING 339 samples in vcf not in ped"

followed by the list of all the samples in the dataset.
I obviously checked if there was any discrepancy between the samples specified in the $VCF and in the $PED, but all the samples seem to match.

Thank you in advance,
Peppe

[Brent Pedersen]

can you show a few lines of your VCF?
and the ped should be tab-delimited and contain 6 columns (family_id, sample_id paternal_id, maternal_id, sex, phenotype) and no genotype information

[Giuseppe1995]

Hi, thank you for the rapid answer!
The problem was indeed the PED file, as I utilized the "raw" PED file resulting from the plink conversion of the VCF (plink --vcf, for the record).

Just for completeness, here follows the code I used to produce a six-column tab-delimited ped file described by you:
let $NEWPED be the variable that indicates the new tab-delimited ped file:
cat $PED | tr ' ' '\t' | cut -f 1-6 > $NEWPED.
I wish I'm not inappropriate by copying my code here, but I just want to help someone that might face the same problem.

Thank you again!

[Brent Pedersen]

great! thanks for posting the code. that will help others who may find this in the future.