Novel Sequence Insertions 1000 Genomes Project
I am looking for novel sequence insertions identified in the 1000 genomes project, and I found 3 files in this...
View ArticleSamtools / Bcftools Missing Random Obvious Single Base Indels
I am using samtools to call variants in a haploid genome (yes I know it is designed for diploid). It finds SNPs easily, and most of the indels, but there are a few indels it can NOT seem to find no...
View ArticleUnknown Indel Notation To Hgvs
I'm sorry about this caotic question, but I don't understand nothing at all... I have a file of Indels finded in genes, presumably from HGMD. Well, i don't know how to read this file, i don't have any...
View ArticleSplit Vcf File Into Snps And Indels
Hi there,As recommended in the GATK best practices the Variant Quality Score Recalibration has to be done separately for SNPs and Indels. But, I didn't find the way to do this split in a clean way (for...
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 ArticleHow To Handle Reads Ending With Deletions In Gatk?
Hello,before asking my question, I should point out that I'm working with data that's not my own (publicly available), to learn and establish a proper workflow when real data wlll arrive in the...
View ArticleGatk Indel Realignment Error - Mismatch In Index Files And Dict File
Greetings,I am aligning pooled sequencing data to a new renferece genome. GATK won't generate intervals because not every scaffold in the reference is found in my bam index?What am I missing? It seems...
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 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As of samtools 0.1.8 'mpileup' appears to have superseded 'pileup' for variant detection.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 ArticleGatk Indel Realignment Taking Forever! Help
Hi all, I am working on exome capture data for barley (1.3Gbp). I am interested in variant calling to find out SNPs in my sample. I have used SAMTools SNP calling and things get done in ~1 hr whereas...
View ArticleFunctional Consequence of In-frame Indel
Does anybody include in-frame indels in association studies? A quick pubmed / google / biostars search on this didn't come up with much. In-frame indels are often treated as synonymous, but since they...
View ArticleCalculating Tn (True Negatives) For An Indel Detection Method
This is a kind of follow-up inspired by the very good question/answers I read in "How to calculate sensitivity/selectivity of an algorithm that returns locations of possible matches?"My goal is 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 ArticleHow To Transform Adjacent Complex Variants In Vcf Format To Individuals'...
Hello, everyone. Recently, I have downloaded the latest variant data of 1000genomes project from ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20110521/ and the mapped data from...
View ArticleGatk Somaticindeldetector Vcf Info Field Missing
Hey everyone,I am a bit confused. I called my INDELs pairwise using the SomaticIndelDetector. But in the resulting VCF the info field seems to be missing, is this normal? Or am I getting something...
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 ArticleDo You Guys Have Any Recommendation On Variant Calling Using Long Contigs Or...
I have assembled a human genome and used bwa mem aligning the contigs back to the reference genome. Do you guys have any recommendation of variant caller?
View ArticleBwa Aln For Snp/Indel Discovery With Paired End 100Bp Human Dna Reads
Hi, Can anyone show me a recommended command line input to achieve this? I have never used the program before and am afraid of entering inappropriate values for one of the many paramters.Or is there a...
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 ArticleDoes Anyone Know Of A Publication Reviewing Snp/Indel Finding Algorithms For...
Hi all, Is anyone aware of a good publication that reviews current methods for detecting SNPs/Indels from next gen sequencing data? I have done some searching but so far in vain. It would be great to...
View Article