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
To anyone who may need to use the ROSMAP imputed data, I used PLINK 2 with the following command to convert the data for each chromosome into PGEN format: ``` for i in {1..22}; do echo "Chromosome $i" plink2 --import-dosage Raw/AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed_chr$i.dosage.gz noheader single-chr=$i format=1 \ --fam Raw/AMP-AD_ROSMAP_Rush-Broad_AffymetrixGenechip6_Imputed.fam \ --out pfile/chr$i done ``` After this step, you can merge all chromosomes into a single dataset using the `--pmerge-list` option. If needed, you can also convert the resulting PGEN files into binary PLINK format by using the `--make-bed` option.
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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