Question: Conversion from plink to merlin failes with Mega2
0
gravatar for Arija
4.9 years ago by
Arija0
Netherlands
Arija0 wrote:

Hi,

I am trying to covert a dataset from plink to merlin format using mega2

parameters are:

Input_Pedigree_File=clean-Z-chr8.hapmap-snps.pruned.fam
Input_Map_File=clean-Z-chr8.hapmap-snps.pruned.bim
Input_Binary_File=clean-Z-chr8.hapmap-snps.pruned.bed
Input_Untyped_Ped_Option=2
Input_Do_Error_Sim=no
Output_Path=.
AlleleFreq_SquaredDev=999999999.000000
PLINK=--bfile --missing-phenotype -9 --trait default
Analysis_Option=Merlin format
Count_Genotypes=4
Count_Halftypes=no

 

During output I receive the folowing errors:

WARNING: calloc allocating no memory at line 761 of file makeped1.c
WARNING: my_calloc called with nelem=0 elsize=4
ERROR: Pedigree 3769 has disconnected individuals (1st one with id 1)
ERROR: For the analysis type specified, a genetic map is required, but none are available in the map file.

I am not sure if this is a memory error, program bug or that I am really missing something in the map file. Can anybody point me in the right direction?

 

plink mega2 merlin • 1.7k views
ADD COMMENTlink written 4.9 years ago by Arija0

Hi, Arija were you able to find a way around the Error related to "Pedigree 3769 has disconnected individuals". I am also trying to convert to Merlin format from Plink and getting the same error!

ADD REPLYlink written 3.8 years ago by kirannarta0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1867 users visited in the last hour