From paper, I have known that the genotyping of the ROS and MAP subjects was performed on the Affymetrix Genome-Wide HumanSNP Array6.0 (n = 1,709) and the Illumina OmniQuad Express platform (n = 384). And
the genotypes were imputed using BEAGLE software.
Therefore, when I download the imputed genotype data online, I found that there are two parts of the imputed genotype data (URL: https://www.synapse.org/#!Synapse:syn3157329) and (URL: https://www.synapse.org/#!Synapse:syn2426141).
Could you please tell me which imputed genotype data should be selected for analysis? or both for analysis? And I also wonder what's the difference between the two imputed genotype data?
Created by xiaoyan li adelalady Unfortunately, those data are missing from the data contributors. We will be releasing another version (imputed to HRC) in the fall. I'm sorry for the inconvenience. Hi,
I can not find the *.fam data (syn2426141) for chop_Illumina which contains 308 individuals. We could know these individual information from the genotype data (syn7824841), but I am not sure the corresponding order in the imputed genotype file.
Thanks
Ting I think you'll need to find that information from the 1000 Genomes Project website. The reference panel used is 1000 Genomes Project Consortium interim phase I haplotypes, 2010-2011 data freeze. Thank you for your reply~ and yes the Plink can read imputation data in a variety of formats including dosage format. And I would like to ask if there is any .map data with imputed dosage format data? The sample files are contained in the same folder. They have extension *.fam. Hope that helps. Thank you for your reply~ and yes the Plink can read imputation data in a variety of formats including dosage format. But I want to get just ped/map format genotype data other than using plink software to analysis something.
And I find the GTOOL software can convert .gen format to ped/map format. And I find that the dosage and gen genotype format are very similar.
But the problem is when I want to add something to dosage file so that can be GTOOL input gen file, I can't known how to do? I don't have sample file for input.
sample_id subject_id missing gender age age_of_onset phenotype_1
0 0 0 1 1 1 P
1A4 W005 0 2 4 -9 0
1A6 W007 0 2 4 -9 0
1A7 W008 0 2 4 -9 1
1A8 W009 0 2 4 -9 1
1A9 W010 0 2 4 -9 1
GTOOL.sample file
SA1 rs001 10000000 A G 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
SA2 rs002 10010000 A G 0 0 1 0 0 1 1 0 0 1 0 0 1 0 0
SA3 rs003 10020000 C T 0 0 1 0 0 1 0 0 1 1 0 0 1 0 0
SA4 rs004 10030000 G T 0 0 1 0 0 1 0 0 1 0 0 1 1 0 0
SA5 rs005 10040000 C G 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1
SA6 rs006 10050000 A G 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0
SA7 rs007 10060000 A C 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
SA8 rs008 10070000 A C 0 0 1 1 0 0 1 0 0 1 0 0 1 0 0
SA9 rs009 10080000 A C 0 0 1 0 0 1 1 0 0 1 0 0 1 0 0
GTOOL.gen file
rs34460896 C T 1.74928 1.78866 1.82217 1.78946 1.78946 1.78577 1.74928
chr15:20001200 G T 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
rs28896870 C T 1.90143 1.91779 1.93001 1.91809 1.91809 1.91679 1.90143
chr15:20001712 G A 1.91167 1.92453 1.93701 1.92481 1.92481 1.92339 1.91167
rs28812614 T C 1.722 1.76445 1.79985 1.76528 1.76528 1.76142 1.722 1.722
rs61999471 T G 1.64523 1.70795 1.74809 1.709 1.709 1.705 1.64523 1.64523
ROSMAP.dosage file Thank you for your reply~ and yes the Plink can read imputation data in a variety of formats including dosage format. But I want to get just ped/map format genotype data other than using plink software to analysis something.
And I find the GTOOL software can convert .gen format to ped/map format. And I find that the dosage and gen genotype format are very similar.
But the problem is when I want to add something to dosage file so that can be GTOOL input gen file, I can't known how to do? I don't have sample file for input.
sample_id subject_id missing gender age age_of_onset phenotype_1
0 0 0 1 1 1 P
1A4 W005 0 2 4 -9 0
1A6 W007 0 2 4 -9 0
1A7 W008 0 2 4 -9 1
1A8 W009 0 2 4 -9 1
1A9 W010 0 2 4 -9 1
GTOOL.sample file
SA1 rs001 10000000 A G 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
SA2 rs002 10010000 A G 0 0 1 0 0 1 1 0 0 1 0 0 1 0 0
SA3 rs003 10020000 C T 0 0 1 0 0 1 0 0 1 1 0 0 1 0 0
SA4 rs004 10030000 G T 0 0 1 0 0 1 0 0 1 0 0 1 1 0 0
SA5 rs005 10040000 C G 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1
SA6 rs006 10050000 A G 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0
SA7 rs007 10060000 A C 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0
SA8 rs008 10070000 A C 0 0 1 1 0 0 1 0 0 1 0 0 1 0 0
SA9 rs009 10080000 A C 0 0 1 0 0 1 1 0 0 1 0 0 1 0 0
GTOOL.gen file
rs34460896 C T 1.74928 1.78866 1.82217 1.78946 1.78946 1.78577 1.74928
chr15:20001200 G T 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
rs28896870 C T 1.90143 1.91779 1.93001 1.91809 1.91809 1.91679 1.90143
chr15:20001712 G A 1.91167 1.92453 1.93701 1.92481 1.92481 1.92339 1.91167
rs28812614 T C 1.722 1.76445 1.79985 1.76528 1.76528 1.76142 1.722 1.722
rs61999471 T G 1.64523 1.70795 1.74809 1.709 1.709 1.705 1.64523 1.64523
ROSMAP.dosage file The data are only provided in dosage format. My recollection is that Plink can read imputation data in a variety of formats and a number of tools are available to reformat genotype files. Thank you for your reply~Another question is whether you have imputed data in plink format? Or could you tell me how to change these raw imputed genotype data to plink format? @adelalady-
The first files come from the Affy chip and the second files come from the Illumina chip, and contain non-overlapping samples.
Solly
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