Hello!
I need to haplotype a patient, their mother, and three or four of the (deceased) father's (living) siblings, so that we can deduce...
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How many SNPs are needed to perform haplotype analysis on close relatives?
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looking for variants only in autosomal chromosomes
Hello!
I'm trying to look for SNPs and indels in a wildcat genome sequenced by our lab, but the problem is that every reference genomes... -
Genotyping using Low-Pass Sequencing data (0.5x - 1x)
Hi all, I am currently trying to do some genotyping using some low-pass sequencing data on 13 1000GP samples. I am mostly interested in biallelic SNPS's.... -
SNP array analysis
I there!!
A friend has passed me the data of an Infinium Omni5-4 array. In short, they have applied two different mutagens to a cell line.... -
SNP array analysis
I there!!
A friend has passed me the data of an Infinium Omni5-4 array. In short, they have applied two different mutagens to a cell line. I have... -
Speciation Genomics course in Berlin
Dear all,
last places left on our Speciation Genomics course with Dr. Mark Ravinet (University of Nottingham, UK) and Dr. Joana I. Meier... -
Post GWAS Interpretation
I’m interpreting GWAS data for a project, from the data I extracted 3 lead SNPs and created LD plots for each using haploview. Now that I have the locations/bp... -
Extract neighbourhood bases of a SNP
I have downloaded the COSMIC mutation data (.maf file). Now for each mutation, I want to extract one base to the left and right of all SNPs. How can I... -
Registration deadline for CBW advanced bioinformatics workshops fast approaching
The registration deadline for the bioinformatics.ca workshops for 2017 is **April 3rd**. Submit an application and a reference letter to apply.
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samtools mpileup
I am new to the file of SNP analysis. Can someone explain me what is the difference between the two callers options (-c and -m) in samtools mpileup? -
RNA-Seq and Variant Analysis Workshop (Aug 29 - Sep 2)
You won’t want to miss our 9th annual Summer Bioinformatics Workshop!
Aug 29 - Sept. 2, 2016
Using Galaxy for Analysis of RNA-Seq,... -
How to get SNP abundance from a metagenomic VCF?
So I have a VCF:
...HTML Code:NODE_2672_length_273_cov_23.978022 190 . G T 275 . DP=217;VDB=3.00218e-07;SGB=-0.477013;RPB=0.289765;MQB=6.34926e-08;MQSB=0.867801;BQB=0.982133;MQ0F=0;ICB=0.78125;HOB=0.111111;AC=8;AN=24;DP4=71,91,23,22;MQ=26
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Strand info, SNPs
Hello,
I am performing an analysis for SNPs in Galaxy UCSC, using the tools mpileup (to generate pileup from bam files) and Varscan (to... -
Filter out 1000 Genomes SNPs from our RNASeq data?
We have RNAseq variant data for 12 tumour samples. We don't have matched non-tumour samples (to filter out germline mutations), so would like to use... -
Tool to estimate genetic heterogeneity using SNP
Hello everyone,
I have a question related to using SNPs as markers of population heterogeneity.
We have four fly strains...
