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• SNP Array data with 0 copies for a segment
  Hello, I am working with SNP array data and would like to know what I should expect to see when ...
• Converting to GDS format
  I'm trying to create nice looking LRR and BAF plots for some SNP array data that I have. I was ho...
• converting Affymetrix SNP 'intensity' data to LRR/BAF data
  Hi all, I am working on a big dataset that used Affymetrix platform for SNP genotyping. I have n...
• Cnv Calling In A Region With Homozygous Snps
  I genotyped 100 samples for CNVs with Taqman Assays and found 6 samples with a heterozygous dupli...
• Calling copy number from SNP arrays
  I have log R ratios and beta allele frequencies from Affy6 data. I've used the LRR with the R pac...
• Calculate LogR ratio and BAF from X and Y intensities
  Hi, Does any one have a recommendation of a method or a program to convert X and Y intensities f...
• Analysis of BAF from SNP array data
  Hi guys, I have a question about the BAF pattern I see when looking at SNP array data. I recently...
• How to Convert Illumina reports to Vcf files?
  Hi All, I am new to CNV analysis and Vcf file conversion. I have an Illumina text report and I ...
• How To Call Cnvs From Raw Intensities
  Dear all, Does anyone have any methods for calling CNVs and/or obtaining LRR/BAF from raw intens...
• Is It Possible To Convert Illumina Genotype Data Into Affymetrix-Like Format?
  I realized that there are many tools only support Affymetrix SNP array data analysis. Is there an...
• Obtaining LRR and BAF values from affymetrix SNP array
  I am trying to extract the `LRR` and `BAF` values from an affymetrix SNP chip without success usi...
• Obtaining LRR and BAF values from affymetrix SNP array
  I am trying to extract the `LRR` and `BAF` values from an affymetrix SNP chip without success usi...
• Circos:- How To Make Circos Histogram Image Using This Data
  Dear all, i am very much new to Circos, able to generate circos image of any table data type bu...
• What are the best tools/practices for CNV (structural variation) detection/analysis for Illumina family data?
  Hi, I am looking for the current state-of-the-art tools/practices for CNV (structur...
• PennCNV and segfault error
  I'm trying to use PennCNV to call CNVs in Affymetrix arrays (Axiom BioBank). After finally compil...
• CNV identified by depth but can not be identified by snp allele frequency
  CNV identified by depth but can not be identified by snp allele frequency. Depth support that the...
• CytoSNP12 minor allele frequency detection levels. How low can we go?
  Ok I a fairly new to both SNV calling and chip arrays. Most of my experience is with RNA-seq, alt...
• Why Penncnv Calcuate Baf As 2 For Some Markers
  Hello Biostars, I am sorry if my question is embarrassingly easy. I was trying to use pennCNV to...
• SNP array liftover data with p values
  Hi, We have canine snp array data (CanineSNPHD, ILLUMINA). The positions of the snps in this arr...