CNV , make GCtype. LRR. BAF files , again

Question

[hosin]

Hi I have three files from a company with following names GCtype, LRR and BAF. But I need to quality control before the analysis ( delete about 100K SNPs). So I think, I should redo the analysis .But I dont know how I can make GCtype, LRR and BAF files after I do the QC (delete) again . Also I have Ped and Map files Please help me

[hosin]

Hello I really appreciate your previous kind help which received through your email Actually I do some QC on the SNPs in Plink. But I dont know how I can extract SNPs for later analysis and re-generating the LRR,BAF files (in fact I want to reduce {remove} a huge amount of Snps in the LRR,BAF files after QC Because too much of SNPs{about100K} should be delete). Please help me? Just I need some commands or examplifing sample of files

Answer 1

[Kevin Blighe]

Hi!

My response on LinkedIn:

Hi Hosein,

The LRR (Log R Ratio) and BAF (B Allele Frequency) files can be used to detect copy number variants, and you should be able to use these in PennCNV: http://penncnv.openbioinformatics.org/en/latest/user-guide/input/#penncnv-input-signal-intensity-files

You should also look at this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015338/

You should also look at the Illumina GEnomeStudio program (software), and these tutorials: https://support.illumina.com/array/array_software/genomestudio/training.html

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The PED and MAP files are the SNP genotype files, and these can be used in Plink. There, you can do some QC on the SNPs, such as SNP and sample missingness, allele frequency, and Hardy Weinberg Equilibrium (HWE): http://zzz.bwh.harvard.edu/plink/summary.shtml

Kevin

For re-generating the LRR, BAF files, etc, look here:

• Generating cluster file and LRR/BAF file