User: aritra90

gravatar for aritra90
aritra9060
Reputation:
60
Status:
New User
Location:
United States
Last seen:
4 months, 1 week ago
Joined:
4 years, 6 months ago
Email:
a*******@gmail.com

Posts by aritra90

<prev • 42 results • page 1 of 5 • next >
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Genome Inflation factor for genomic control too large
... Hi, I am trying to do genomic control on the simulated data generated from the Balding-Nichols model (Fst = 0.01) on two populations. The lamba which I am obtaining after dividing the median chi sq statistic on all of the SNPs by median of chisq(1) is quite big. The p-value threshold I've set is ...
gwas plink genomics snp stratification written 7 months ago by aritra9060
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How to force missing values for genotype?
... Hi, I was wondering how to force missing values in genotypes in PLINK format files? I tried doing `--update-alleles` followed by `--recode` but that didn't work. I want to force some arbitrarily chosen marker's genotype values for some individuals to 0 (missing). In other words, I want to **mask ...
plink snp genotypes written 8 months ago by aritra9060 • updated 8 months ago by zx87548.8k
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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 14 months ago by aritra9060
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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 14 months ago by aritra9060
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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 14 months ago by aritra9060
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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 14 months ago by aritra9060
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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 2.5 years ago by aritra9060
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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 2.5 years ago by aritra9060
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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 2.5 years ago by aritra9060
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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 3.1 years ago by aritra9060

Latest awards to aritra90

Popular Question 13 months ago, created a question with more than 1,000 views. For PLINK: removing SNPs missing in all samples
Popular Question 13 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 2.5 years ago, created a question with more than 1,000 views. For EIGENSOFT: CONVERTF ignoring samples
Popular Question 2.5 years ago, created a question with more than 1,000 views. For PLINK: removing SNPs missing in all samples
Popular Question 2.5 years 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 2.7 years ago, created a question with more than 1,000 views. For PLINK: removing SNPs missing in all samples
Popular Question 3.1 years ago, created a question with more than 1,000 views. For PLINK Merge error: File write failure
Popular Question 3.1 years ago, created a question with more than 1,000 views. For EIGENSOFT : Ploteig, 3D Plots
Popular Question 3.2 years ago, created a question with more than 1,000 views. For EIGENSOFT : Ploteig, 3D Plots
Popular Question 3.8 years ago, created a question with more than 1,000 views. For EIGENSOFT : Ploteig, 3D Plots
Popular Question 3.8 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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