Sequence Variation Detection For Prokaryotic Genomes
I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).Which...
View ArticleCan´T Find The Snps With Samtools (Only Get Indels)
Hello everybody, Could anyone tell me how to get SNPs using SAMtools???. I am learning how to do it but can´t get the SNPs, I only get the Indels. I am working with a mutant I created from an E coli...
View ArticleFrequency Of Homozygous Indels Vs Heterozygous Indels
I have been surprised to read in Genetic Variation in an Individual Human Exome that most of indels in coding regions are homozygous:The HuRef genome contains a total of 739 coding indels, which...
View ArticleSnps And Indels In Homozygous Genomes
I have a genomic sequence of an inbred mouse strain i.e. the genome is homozygous for a given position or same alleles are present on both of the strands. Now for variant calling, I have to compare it...
View ArticleTool: Phylosim - Monte Carlo Simulation Of Sequence Evolution In The R...
PhyloSimPhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses...
View ArticleExtracting Specific Reads From Vcf File
Hello,I am trying to extract indels with coverage ~1 and they are in a VCF file. How do I write a python script or a shell commnad to extract those indels with coverage 1 only? This is the data:chr1...
View ArticleTrio: Detecting A Large De Novo Indel
I've been given a set of three BAM (father, mother, child) and I expect the child to contains some de-novo heterozygous variations . samtools mpileup have been used to find the small variations but...
View ArticleTool For Finding Indel In Which Part Of Genes
Are there any tools to help us determine whether an indel lies within a specific part of the gene ( Exon, Intron, ...)?
View ArticleHow Do You Do Local Realignment Around Indels For Exome Sequencing?
Hi all, I am wondering how people generally go about local realignment around indels in their workflow? The most popular programs seem to be SRMA and GATK - does anyone use anything else?In my initial...
View ArticleIndel Detection For 454 Resequencing
I do some work for a small diagnostics company that has a requirement for small indel detection in 454 data. Those of you familiar with Roche's pipeline will be aware that AVA (Amplicon Variant...
View ArticleClik here to view.
Indel Left/Right Alignment
When matching indels between different VCF files (generated by different callers), there is this issue with left / right indel alignment, For example: Here is a real example for one indel (from the...
View ArticleVcf Snps And Indels Mouse Genomes
Hi, I am using SNPs and INDELs data from the mouse genomes project and the data seem to have conflicting information. I mean, seems they report a SNP in a deleted position. Thus my question, Is it...
View ArticleInsertion Detection Tools
Hi,Please suggest me some tools which can detect large indels (esp. of size > 100bp). Some of the tools I have already tried include Breakdancer and Pindel and Hydra. Any other suggestions??
View ArticleFiltering Vcf File
I was wondering how to filter the vcf file based on a few input arguments ( DP>10, MQ>30 and QD>20 or GT = "1/1" etc)? I m planning to use simple command on the command line to extract the...
View ArticleHow Best To Add Custom Variation Track To Ucsc Browser?
I have generated sequence variants (SNPs/INDELs) by NGS resequencing and would like to display them on the UCSC browser (I have resequenced against a UCSC reference genome). Obviously i could use BED...
View ArticleGatk Threshold Parameter For Clipping Of Reads During Indel Calling Running...
GATK 1.6 claims to apply a Q20 threshold to clip ends of the reads for the indel caller:http://www.broadinstitute.org/gatk/guide/article?id=12373. Indel Calling with the Unified Genotyper [...] while...
View ArticleWhat Approach Would You Recommend For Large Indel Detection With Solid Data
I've been spending quite some time on following problem: I sequenced a bacterial genome using paired-end reads (SOLiD) and I have a quite good reference sequence. My goal is to detect changes in the...
View ArticleHow Many Is Too Many? Germline And Somatic Coding Indels And Snps In Cancer...
Would anyone care to share their experience with variant calling in cancer genomics using tumor - normal pair to find somatic vs germline variants especially indels?I have been getting an unbelievably...
View ArticleBest Way To Compare Output Snp/Indels From Different Software?
I have a list of SNPs and indels from 4 different software. IndelGenotyper (broad tool)—for calling somatic indels Bambino—for calling SNP/Indels Somaticsniper—SNP calling Varscan – indel/snp/LOH Now...
View ArticleChip-Seq Peak Caller Able To Find Peaks Split By Indels?
Are there any chip-seq peak callers able to find cases where the region under a peak has been split by an indel between the reference and the chipped sample?For example, let's suppose one has done...
View Article