Is there any way to quantify differences between neighbour-joining...
I am working on a project and I am currently only using the SNP data to make my trees. I would like to compare the trees made using SNP data to the trees made using indel data to ensure they are...
View ArticleWhole Genome Dna Amplification Before Applying Wgs
Dear allWe have some DNA samples that I would like to run whole genome sequencing on. Unfortunately these samples only contain very little DNA (too little for WGS). It has then been suggested to do...
View ArticleHow To Make A Circular Plot Of Snps And Indels ??
Hello everybody,I am analysing SNPs and INDELs in several prokaryotic genomes of the same strain. My goal is to compare them with a reference genome . I would like to learn how to plot the SNPs in a...
View ArticleHow To Calculate Genotype Concordance Between Indel Call Sets?
How do people calculate genotype concordance between INDEL call sets? I have a NGS and BAC based INDEL call set (in vcf) but I get a higher false positive and false negative rate than mentioned in some...
View ArticleHow To Call Snp And Indel Based On A Sanger Sequences Based Bac Contig Vs...
I have BAC contig, assembled from sanger sequences, that I want to use for quality control on my short read based SNP and indel call's.Which tool can I use to align the BAC sequence against the...
View ArticleClassify Mutations Which Are Found Ny Using Exome Sequencing
Hi, everyone. I used exome sequencing to sequence tumor and blood, and after I remove mutations in blood and snp in dbsnp131, I found I still have about 2000 mutations. I read the exome sequencing...
View ArticleIs It Possible To Get Rs Numbers For Indels?
I am currently designing an Illumina custom GoldenGate platform (for the first time, so with lack of experience..). I have finished the selection of SNPs and I'm ready to submit the list for...
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 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 ArticleSamtools: Local Realignment Around Indel
In samtools mpileup, adjust the option -m and -F to control when want to initiate indel realignment, any guideline to set the values for m and F for high coverage data (eg. >=20X)low coverage data...
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 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 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 ArticleGenomic Alignment And Snp/Indel Calling - My First Ever "Pipeline"
So I have finally generated some reads and run it through what I guess could be called a very rudimentary 'pipeline'. I generated a million paired end reads with wgsim then aligned with bwa, and used...
View ArticleTools For Large Indels Discovery In Single-End Rna-Seq Reads
Hi all,Has anyone heard about any tool wich could deal with large indels discovery? I've found some for paired-end reads but never for single-end... My final goal is to find transposable elements...
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 ArticleIndel Notation In Variant Calling
HelloI am sorry for the basic question but I am struggling to find any details of the nomenclature of indels by variant calling software. Unfortunately i am unable to access the details of the software...
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 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...
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