User: User 1933

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User 1933340
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4 years, 8 months ago
Joined:
7 years, 7 months ago
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g*******@magooli.com

Posts by User 1933

<prev • 83 results • page 1 of 9 • next >
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Comment: C: A Shift In Pca Plot For Population Stratification
... yes, there are 1212 individuals in 1KG which are represented by black in the plot. mm, the 1KG sequencing has been done both with Illumina and ABI sequencing; I feel I should have normalize these two cohort separately somehow before hand. ...
written 4.7 years ago by User 1933340
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10 follow
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A Shift In Pca Plot For Population Stratification
... To do the population comparison between cohort of patient and 1KG. So, I have converted their VCF file to PED format; vcftools --gzvcf 1000g/1000g_myvariants.vcf.gz --plink --out 1000g vcftools --vcf myvariants.vcf --plink --out myvariants and then, I took variant with snp ID grep -o 'rs[0-9]*' ...
exome-sequencing pca written 4.7 years ago by User 1933340 • updated 3.5 years ago by Zhenyu220
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Comment: C: Variant Function Prediction
... seems they don't work with hg19 - but thank you in any case ...
written 4.7 years ago by User 1933340
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Comment: C: Variant Function Prediction
... that is same as SIFT and Polyphen 2 ...
written 4.7 years ago by User 1933340
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Variant Function Prediction
... Basically, I would like to know what are some variant function/effect predictor ? I already know SIFT and Polyphen and mutationassessor. I was curious if there is any other that I have missed. ...
variant effect snp written 4.7 years ago by User 1933340 • updated 2.7 years ago by christopher medway420
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Comment: C: Pca From Vcf Files
... you meant autosome.only=FALSE ? since TRUE returns the same error ("Removing 362090 non-autosomal SNPs. - there is no SNP") ...
written 4.7 years ago by User 1933340
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Calculating Sequencing Depth Of A Genomic Region
... In an whole-exome study project, I need to calculate the sequencing depth for a given set of genes. It seems DepthOfCoverage from GATK can do this for me. However, I am curious if I can get the similar information from the VCF file ? Alternatively is there any other tool I can use ? ...
vcf exome-sequencing written 4.7 years ago by User 1933340 • updated 4.7 years ago by Alex Paciorkowski3.3k
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Comment: C: Length Of The Longest Available Cdnas For Gene Set
... Isn't there any public dataset to include the cDNA size of any gene ? ...
written 4.9 years ago by User 1933340
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Comment: C: 1000 Variant Calling Parameters
... I am looking at the significance of new variants/of the variants. Thank you any way ...
written 4.9 years ago by User 1933340
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For One Hugo Id Several Ensemble Id - In 1Kg
... I am querying 1KG based on hugo ID, and I noticed that, for some of the genes, there are several entries with different ensemble ID. I appreciate if someone can make comments on that, for example, if you look into CFB in the 1KG, (click here) several different ensemble id are assosiated to this Hug ...
1000genomes written 4.9 years ago by User 1933340 • updated 4.9 years ago by aheinzel110

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