User: aritra90

gravatar for aritra90
aritra9020
Reputation:
20
Status:
New User
Location:
United States
Last seen:
4 months, 4 weeks ago
Joined:
3 years, 9 months ago
Email:
a*******@gmail.com

Posts by aritra90

<prev • 40 results • page 1 of 4 • next >
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Comment: C: Prune SNPs in LD with a list of SNPs
... I couldn't figure out the right command to enter a SNP list and a genotype file and obtain another snp list which are in high LD. For now I've been using indep-pairwise to remove the SNPs in high LD beforehand and then do downstream analyses. However, I wanted to remove SNPs which are in LD with a p ...
written 5 months ago by aritra9020
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Prune SNPs in LD with a list of SNPs
... Hi, I have a list of SNPs. I want to find the SNPs in a genotype (Plink format) data set, which are in LD (> 0.2) with the list of SNPs. Any help on how to achieve this is appreciated. Thanks. ...
snp plink ld written 5 months ago by aritra9020
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Comment: C: VCF filtering based on AB (Allele-Balance) tag
... Thanks a lot @AISHA! Your description and that link is really helpful! ...
written 5 months ago by aritra9020
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Comment: C: VCF filtering based on AB (Allele-Balance) tag
... Hi @AISHA, just want to understand the rationale behind the above command in retaining the homozygous calls. Piping AB < 0.01 makes you retain the homozygous calls? What if I want to filter by AB in homozygous calls as well as retaining heterozygous ones? ...
written 5 months ago by aritra9020
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Merging a PLINK file with itself after duplicating sampleIDs and rsIDs
... Hi, I want to merge a PLINK file with itself, maintaining high genotyping rate. Let's say I have a file test.bed/bim/fam, what I am doing is the following: 1. randomly selecting few SNPs from test.bim into a file snpstoflip.txt 2. flipping those SNPs using ./plink --bfile test --flip snpst ...
merging plink snp genotype written 21 months ago by aritra9020
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Comment: C: Maximum amount of data that smartPCA program can process?
... True that, that's a typo on my part! ...
written 21 months ago by aritra9020
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Maximum amount of data that smartPCA program can process?
... Hi, I was curious to know what is the maximum amount of data that the EIGENSOFT package can process, specifically the smartPCA program. The page says about "special care" for upto 8 bil. genotypes, however, that is specified for the QTL program. I was more interested in just obtaining the PCs alon ...
eigensoft pca genotype snp smartpca written 21 months ago by aritra9020
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Merging data with b37 and hg19
... Hi, I want to merge two PLINK binary files, one is hg19 build and the other is dbSNPs b37. How should I go about merging these two ? It'd be great if you guys can help. Thank you. ...
genome plink snp written 2.4 years ago by aritra9020
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Comment: C: PLINK --within flag not clustering all of the samples
... Hi, I have mailed you all the files but got a failure mail from the mail delivery system saying probably it's over quota. It'd be great if you look into it or if you have an alternate email. Regards, Aritra ...
written 2.5 years ago by aritra9020
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Comment: C: PLINK --within flag not clustering all of the samples
... Hi, Should I mail you at chrchang@alumni.caltech.edu ? Please let me know otherwise. Thanks a lot for the prompt response. ...
written 2.5 years ago by aritra9020

Latest awards to aritra90

Popular Question 21 months ago, created a question with more than 1,000 views. For EIGENSOFT: CONVERTF ignoring samples
Popular Question 21 months ago, created a question with more than 1,000 views. For PLINK: removing SNPs missing in all samples
Popular Question 21 months ago, created a question with more than 1,000 views. For Understanding AWClust's SNP file data format and converting a PED file to it
Popular Question 23 months ago, created a question with more than 1,000 views. For PLINK: removing SNPs missing in all samples
Popular Question 2.4 years ago, created a question with more than 1,000 views. For PLINK Merge error: File write failure
Popular Question 2.4 years ago, created a question with more than 1,000 views. For EIGENSOFT : Ploteig, 3D Plots
Popular Question 2.4 years ago, created a question with more than 1,000 views. For EIGENSOFT : Ploteig, 3D Plots
Popular Question 3.1 years ago, created a question with more than 1,000 views. For EIGENSOFT : Ploteig, 3D Plots
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Compare consecutive columns of a file and return the number of non-matching elements

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