User: tarek.mohamed
tarek.mohamed • 0
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Posts by tarek.mohamed
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... 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.mohamed • 0
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... Hi All,
What is the best way to compare genotypes between two different vcf files.
Thanks
Tarek ...
written 6 days ago by
tarek.mohamed • 0
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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.mohamed • 0
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... 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 ...
written 7 days ago by
tarek.mohamed • 0
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... 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.mohamed • 0
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... Hi Ahil,
How can I compare genotypes in two ped files?
Regards,
Tarek
...
written 8 days ago by
tarek.mohamed • 0
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... 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.mohamed • 0
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... 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 ...
written 12 days ago by
tarek.mohamed • 0
• updated
12 days ago by
chrchang523 • 2.6k
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... 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.mohamed • 0
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... 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;
...
written 23 days ago by
tarek.mohamed • 0
• updated
23 days ago by
Zev.Kronenberg ♦ 11k
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