User: tarek.mohamed

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Posts by tarek.mohamed

<prev • 45 results • page 1 of 5 • next >
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Comment: C: compare genotypes in two vcf files
... Hi Pierre, I have only one sample per vcf file. Basically, I has genotype calls from illumina final report, then I converted them to ped then to vcf files. Thanks Tarek ...
written 5 days ago by tarek.mohamed0
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compare genotypes in two vcf files
... Hi All, What is the best way to compare genotypes between two different vcf files. Thanks Tarek ...
genotypes compare vcf files written 6 days ago by tarek.mohamed0
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Comment: C: lgen to ped using plink
... Hi Chang, Thanks again for the reply. You are right, this discrepancy is due to the unsorted map file. After comparing ped file with a sorted map file, everything seems to be fine now. Tarek ...
written 7 days ago by tarek.mohamed0
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lgen to ped using plink
... Hi All, How can I create a lgen file which has only one individual genotyped for 300,000 SNPs. I mean in the context of sample ids, what shall I use? I created the lgen, fam files below. Then I used plink 1.9 to generate ped file (log file shown belos). The problem is that genotypes in ped file mism ...
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Comment: C: illumina genotype reports _lgen to ped using plink
... Hi Christopher, How can I create a lgen file which has only one individual genotyped for 300,000 SNPs. I mean in the context of sample ids, what shall I use? I created the lgen, fam files below. Then I used plink 1.9 to generate ped file (log file shown belos). **The problem is that genotypes in p ...
written 7 days ago by tarek.mohamed0
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Comment: C: Compare genotypes from sequencing (vcf) and microarrays (ped)
... Hi Ahil, How can I compare genotypes in two ped files? Regards, Tarek ...
written 8 days ago by tarek.mohamed0
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Comment: C: illumina genotype reports _lgen to ped using plink
... can you send me the link for this newer build. Also, can I do this with plink2? I searched plink2 but I could not --file flag Thanks ...
written 12 days ago by tarek.mohamed0
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illumina genotype reports _lgen to ped using plink
... Hi All, I have an illumina genotype final report, and I want to convert it to .ped using plink. I prepared three files; fam, lgen, and fam (please find below a snap shot for these files ) Then I used plink, but O got the error **Variant 'rs1000002' in .lgen file has 3+ different alleles.** Althoug ...
ped lgen illumina genotype report plink written 12 days ago by tarek.mohamed0 • updated 12 days ago by chrchang5232.6k
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Comment: C: comparing two illumina genotypes report
... Hi Kronenberg, Thanks for the reply! What would be the best way to convert illumina genotype report to VCF? Regards Tarek ...
written 14 days ago by tarek.mohamed0
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comparing two illumina genotypes report
... Hi All, I have two final illumina reports from bead chip experiment (300,000 SNPs). Ideally genotypes of these two samples should be identical. How can I compare between the genotypes of the two samples to see if they are really identical or there are some mismatches? The files look like this; ...
gtc_files written 23 days ago by tarek.mohamed0 • updated 23 days ago by Zev.Kronenberg11k

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