What Is The Best Tool For Mouse (Mm9 Or Mm10) Variant Annotations?
I am working with some mouse exome capture data, and I would like to provide functional annotations to variants (SNPs and small indels).For human data, I would typically use ANNOVAR. It looks like...
View ArticleNext Gen Sequencing Indel Realignment With The Genome Analysis Toolkit (Gatk)
As I continue to add steps to my SNP/Indel discovery workflow, the latest recommendation is local realignment around Indels using GATK following the initial alignment step. I have just commenced the...
View ArticleMulti-Sample Indel Realignment Using Gatk
Is there a way to use the GATK Indel Realigner tool with a two-samples-input? The issue is that in my normal sample, several reads are mapped containing SNPs at specific positions, and ONE read having...
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 ArticleGatk3 Vs Dindel For Small Indel Calling
I read some posts from Heng Li around two years ago that he suggested Dindel is the optimal software for small indel calling. I'm just wondering if this is still true today because GATK seems to...
View ArticleHow Does Left-Alignment Work For Indels? Does It Address All Complicated...
I can vaguely guess its meaning but want to know, at least, how it works in different situations. Besides, after left alignment, can we write an indel in VCF file in a unique way?Thank you!
View ArticleWhat Is The Difference Between Samtools Mpileup And Pileup
As of samtools 0.1.8 'mpileup' appears to have superseded 'pileup' for variant detection. The samtools website now has pileup as deprecated. So i am wondering whether i should repeat my recent...
View ArticleWhat Is Difference Between Gatk And Dindel For Calling Indel
What is difference between GATK and Dindel for calling indel ,I see that in the GATK second step :discovery indel ,The genotype likelihoods calculation is inspired by Dindel.So I want to know the...
View ArticleMerging Vcf Files And Filling In Missing Genotypes
I have vcf files with genomic variants (e.g. SNPs and Indels) from several patients. I now want to merge them into one vcf file e.g. using vcftools' merge-vcf. Doing that I get a file that holds for...
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 ArticleBenchmarking Read Alignment And Variant-Calling Algorithms (For Dummies)
Hi all, I am wondering if there is a good step by step guide of how to benchmark alignment and variant calling software. I do understand the premise e.g.Generate reads with known mutations Align to...
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 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 ArticleAnyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
I'm looking for a general variant annotator ... one that would call a variant as synonymous, non-synonymous, non-genic, UTR, frame-shift, truncation, etc. By general I mean that we should be able to...
View Article1000 Genomes Indel/Snps File
Is there any place to download 1000 genome SNPs and Indels data in a single merged file for each pilot (pilot 1 , 2 , and 3) ? I am trying to use GATK and thought to use 1KG indels and SNPs vcf files...
View ArticleIs There A Convention For Representing Indels In Diploid Genome Sequences?
If an individual has a heterozygous indel how should that be represented in a sequence?I am looking for some examples along the lines ofA[C]GT or A[C/-]GT
View ArticleStructural Variation Detection On A Short Reads Simulation
Hi,I am trying to do the following exercise (still playing with indels):simulate short reads (and indels) out of a human genome chromosome,align the short reads simulated in (1),call indels using a SV...
View ArticleHow To Detect Overlaping Indels In Vcf File?
Hi all,I have a vcf file with indels from a whole genome analysis and I want to detect overlapping between indels... I tried to use BEDtools-intersect but it asks for 2 files, and I only have a single...
View ArticleSimulating A Read With A Deletion Of 50 Bp Into It.
Im trying to test some indel calling programs with large deletions in sequencing reads. I ve got this sequence in Chromosome 20 of hg19 : > CTAGCAAGGG GGCTGTATGG CTTGAGGCCA TAGTCCAGGA CATCATCGGG...
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 Article