Hello,
I'm looking for a tool to call somatic single nucleotide variations on reads from an ONT run.
I have both tumor and normal samples...
12 results in 0.0028 seconds.
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somatic SNV tool for ONT samples
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calling SNVs in shallow WGS data from liquid biopsy
Hi All,
could there be any reasonably reliable SNV calling approach in the following scenario: I have shallow (1-3x) WGS sequencing data... -
How can i adjust the VAF values based on newly correctly estimated tumor purity
I have been provided with a MAF file which includes the VAF for each SNV. However, purity was incorrectly estimated and then the newly corrected estimated... -
Amplicon based sequencing Mutation Calling
Hi!
We are investigating the effect of TF-mediated mutations on genome. In the validation part, we narrowed our regions to 1. We sequenced... -
Tumor-only variant calling
I'm attempting to call SNVs in tumor samples without a paired normal sample. Some of these tumor samples can have low purity, so the allelic frequency... -
SNV ignored by bcftools
Hi everyone,
I am currently using bcftools to call variants and saw some strange behavior. It would be perfect if someone could explain...Last edited by behrj; 11-25-2014, 06:18 AM. -
Virmid - SNV mutation caller
Anyone here have any experience using Virmid? I have some exome seq data that I want to use it on but on first attempt with default parameters I get this... -
vcf file filtering looking for polimorphisms
Hi everyone:
I recently got my mpileup-bcftools results looking for SNV's on a ~200 sample population. It happens that there is no reference... -
Validation by genotyping arrays (SNP arrays) - why only heterozygous SNPs?
Hi,
I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications...Last edited by ak352; 09-16-2013, 04:53 AM. -
How to calculate nucleotide diversity from SNP data from multiple samples
Hi all,
I have a collection of SNP data from a tetraploid population, and I would like to calculate the nucleotide diversity. The generel forumula... -
GATK to discover Single Nucleotide Variation in mature miRNA from miRNA-Seq
Hi,
for my final project, I am looking for Single Nucleotides Variants in mature miRNA starting from an experiment of miRNA-Seq on different cancer... -
wet lab Validation of a large number of SNPs
Hi
AFAIK
you can validate SNPs obtained by Hi-seq by
microarray,
Sanger Seq,
NGS seq on a different platform ...
