Quality check for illumina GSA data

Dear all, I have many illumina GSA (iscan) data, I would like to check is these any sample contaminated? Is there some tool in linux could do in command line? Thanks and with best regards, Xinhui

snps illumina

• 2,223 views • link

updated 5.8 years ago by brinderbuttar •

• written 9.1 years ago by xinhui.wang

1 answer

Hi Xinhui, I am also looking for solution to the problem you shared few years back. I suppose you might figured out the answer also. People are recommending PLINK for that, if you have anything else, please let me know. Thanks in advance Brinder

• 0 views • link

written 5.8 years ago by brinderbuttar •

More posts like this

how to convert from CpG island methylation array ID to target ID?
written 4.5 years ago by xinhui.wang

Dear all, I have a list of CpG island methylation array IDs, like "CHR0100P000018599", I would like to convert these IDs into target IDs as …
how to assembly the RNASeq data
written 5.9 years ago by xinhui.wang

Dear all, I have some RNA short RNAseq (mouse) data and I would like to get the LncRNA and mRNA from these seqs with MM10, …
how to adjust a phenotype according to age
written 7.3 years ago by xinhui.wang

Dear all, I am running an analysis on one phenotype and many SNPs with random forest. However, I find that phenotype correlated with age. I …
How to generate genetics risk score with linkage disequilibrium?
written 9.2 years ago by xinhui.wang

Dear all, I am working on genetics risk score generation with many SNPs on certein diseases. Our previousl algorithm is based on weight GRS, however, …
genetic risk score generation with LD
written 9.3 years ago by xinhui.wang

Dear all, I am trying to generate genetics risk score with about 20 SNPs, however, I tried to combine LD structure (or Block) to generate …
risk value with genetic data
written 9.7 years ago by xinhui.wang

Dear all, I am working on diagnositc work. I check the expression of may SNPs and would like to give a risk value from these …
Haplotype Association Tests
written 11.1 years ago by xinhui.wang

<p>Dear all,</p> <p>I am runing assocation analysis with PLINK. I need to test the effect of combination of SNP's effect, or haplotype association analysis. Unfortunately, …
How to extract sample id using bcftools or vcftools
written 11.3 years ago by xinhui.wang

Dear all, I am working on vcf data with *bcftools*. It is a big data set and I would like to see the list of …
how to calculate the accuracy of imputation?
written 11.3 years ago by xinhui.wang

<p>I run bingle 4.0 to imputate some chip snps to GWAS. After that, I would like to check the accuracy (quality) of my imputation. I …
How to extractreference allele from fasta file
written 11.4 years ago by xinhui.wang

I am running vcftools to get ped file from a list of vcf files. I would like to know the reference allele for these snps …