how to calculate BAF and LRR from bam or vcf file
How can i calculate LRR and BAF from bam or vcf file for WGS data?
lrr
baf
bam
vcf
• 1,753 views
•
link
updated
by
4galaxy77
288
• |
written
by
BioKeystone
0
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Difficulty Finding LRR SD and BAF Drift in GenomeStudio 2.0
written by Josephine H. 0Hello everyone, I need some help with GenomeStudio: where I could find the Log R ratio Standard Deviation (LRR SD) and B allele Frequency Drift …
-
Axiom PMRA cel files to VCF format
written by a.papadam 0Hello all, I am currently trying to convert CEL files from Axiom PMRA chip to VCF format. A VCF that will need to include also …
-
how to calculate BAF and LRR from VCF or BCF files?
written by xiaoguang 16Hi, Do anyone know how to calculate BAF(B-allele frequency) and log R ratio from SNP calling pipeline( bcftoools mpileup & call) ? I read some …
-
How can I create an Illumina report in Linux using IDAT files?
written by Ginevra 1Hello everyone! I am looking for a way to create an Illumina report, starting from IDAT files. I know how to do it with GenomeStudio …
-
get B allele frequency (BAF) and lor R ratio (LRR) in LINUX
written by cocchi.e89 30Dear all, I know I can obtain the BAF and LRR from raw data on Illumina GenomeStudio software, but it works on Windows. How about …
-
CNV , make GCtype. LRR. BAF files , again
written by hosin 0Hi I have three files from a company with following names GCtype, LRR and BAF. But I need to quality control before the analysis ( …
-
LRR and BAF calculate
written by taghizadehkobra 0how can i calculate LRR and BAF for Illumina SNP arrays?i m trying to work on snp chip data
-
converting Affymetrix SNP 'intensity' data to LRR/BAF data
written by nikman.nor-hashim12 0Hi all, I am working on a big dataset that used Affymetrix platform for SNP genotyping. I have never worked on Affymetrix-related genotyping datasets. What …
-
Calculate the b allele frequency from a VCF file
written by Maj 0Hello, I have to calculate the b-allele frequency from a vcf file. But I have some problems to understand some genotypes. For example : 1/1:17:283,34,24:**2,15**:69,68 …
-
Tools to view LRR and BAF for Illumina SNP arrays
written by ebrown1955 32<p>Are there any tools (free) that can view BAF and LRR for Illumina SNP array data? I'm trying to visualize specific regions quickly and easily.</p>
Can you define those acronyms please.
BAF b allele frequency LRR log R ratio
Need more details. There is no accepted definition of what a 'b allele' is - how are you defining it? And the log ratio for what?