[#2664] export.merlin produces incorrect ped files.

Date:
2013-04-04 15:35 Priority:
4

State:
Open

Submitted by:
Daniel Taliun (dtaliun) Assigned to:
Lennart Karssen (lckarssen)

Resolution:
Accepted As Bug Operating System:
Linux (64bit)

Severity:
major Hardware:
All

Version:
v1.8-0 Component:
GenABEL

URL:

Summary:
export.merlin produces incorrect ped files.

Detailed description
GenABEL v. 1.7-4 (February 22, 2013) When exporting a subset of individuals from gwaa.data with export.merlin, the genotypes in ped files are incorrect. Additionally, ped files produced by analogous commands export.merlin(df[ids, snps], datafile=data_file_name, pedfile=ped_file_name, mapfile=map_file_name, order=T, fixstrand="+", stepids=1) and export.merlin(df[ids, snps], datafile=data_file_name, pedfile=ped_file_name, mapfile=map_file_name, order=T, fixstrand="+", stepids=100) are not identical. When stepids=1, the ped file seems to be correct. This behavior is observed only with subset of ids. When gwaa.data is exported completely, the everything is ok.

Comments:

Message
Date: 2015-07-30 05:35 Sender: Nadezhda Belonogova Sorry for the appearance of the previous post, all paragraph break signs are gone. I am not yet familiar with this message service.
Date: 2015-07-30 05:24 Sender: Nadezhda Belonogova For example, correct genotypes in merlin.ped (exported with stepids = n) are: 1 id1 0 0 2 0 T/T C/C G/G G/G G/G ... 2 id2 0 0 2 0 T/C C/C G/G G/G G/G ... 3 id3 0 0 2 0 T/T C/C G/G G/G G/G ... 4 id4 0 0 2 0 T/T C/C G/G G/T G/G ... 5 id5 0 0 1 0 T/T C/C G/G G/G G/G ... 6 id6 0 0 2 0 T/C C/C G/G G/G G/G ... 7 id7 0 0 2 0 T/T C/C G/G G/G G/G ... 8 id8 0 0 2 0 T/T C/C G/G T/T G/G ... 9 id9 0 0 2 0 T/C C/C G/G G/G G/G ... 10 id10 0 0 2 0 T/T C/C G/G G/G G/G ... ... With default stepids = 100, genotypes look strange for all markers starting from the second one: 1 id1 0 0 2 0 T/T C/C G/G G/G G/C ... 2 id2 0 0 2 0 T/C 0/0 G/G G/G G/G ... 3 id3 0 0 2 0 T/T 0/0 G/G G/G G/G ... 4 id4 0 0 2 0 T/T 0/0 G/G G/G G/G ... 5 id5 0 0 1 0 T/T C/C G/G G/G G/C ... 6 id6 0 0 2 0 T/C C/C 0/0 G/G G/G ... 7 id7 0 0 2 0 T/T C/C 0/0 G/G G/C ... 8 id8 0 0 2 0 T/T C/C 0/0 G/G G/G ... 9 id9 0 0 2 0 T/C C/C G/G G/G G/C ... 10 id10 0 0 2 0 T/T C/C G/G 0/0 G/C ... ... The number of genotypes is correct, .map and .dat files are ok and keep the same order of markers. In addition, I tried to reproduce a bug on a small sample and found that it appears only with n > 1000.
Date: 2015-07-29 20:08 Sender: Lennart Karssen Thank you Nadezhda, for reporting this here. Also thanks for providing a workaround. Can you be a bit more specific about "genotypes are totally wrong"? Do I understand correctly that genotypes are written to the merlin file, but that they are not the correct genotypes? Is the total number of genotypes correct? I have re-opend the bug and increased it's severity.
Date: 2015-07-29 04:06 Sender: Nadezhda Belonogova Just found out on my data that genotypes exported by export.merlin() are totally wrong (GenABEL_1.8-0). Setting 'stepids = n' where n is the sample size seems to work fine.
Date: 2013-06-03 12:56 Sender: Lennart Karssen Addendum to my previous comment: the unit test was added in svn r.1242.
Date: 2013-06-03 12:48 Sender: Lennart Karssen I tried to confim this bug, but wasn't able to (GenABEL v1.7-6). Just to be sure I added a check test.export.merlin.bug2664() in the unit tests to make sure it doesn't pop up again. Marking this bug closed. Feel free to re-open it if the problem appears again.
Date: 2013-05-16 16:32 Sender: Lennart Karssen Since export.plink() calls export.merlin() when not writing tped files, bug #2055 may be related.

Attached Files:

Changes

Field	Old Value	Date	By
Resolution	Works For Me	2015-07-29 20:08	lckarssen
Severity	None	2015-07-29 20:08	lckarssen
Version	v1.7-4	2015-07-29 20:08	lckarssen
status_id	Closed	2015-07-29 20:08	lckarssen
close_date	2013-06-03 12:48	2015-07-29 20:08	lckarssen
priority	3	2015-07-29 20:08	lckarssen
status_id	Open	2013-06-03 12:48	lckarssen
close_date	None	2013-06-03 12:48	lckarssen
assigned_to	none	2013-06-03 12:48	lckarssen
Resolution	None	2013-06-03 12:48	lckarssen
Hardware	None	2013-06-03 12:48	lckarssen
Version	None	2013-06-03 12:48	lckarssen