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 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 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 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 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 ArticleDeletions, Translocations And Cnv From Rna-Seq
Is it possible to find out deletions tarnslocations and / or copy number variations between RNA-seq data of control vs treated samples. The data is PE with enough coverage ( say around 30X).Thanks
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 ArticleHow Are Indel Coded In Vcf Files
Hello,I have a question concerning how are INDEL coded in VCF files. I have for instance the following file:CHROM POS ID REF ALT QUAL FILTER8 18078835 . TTA T 46 PASS8 18078836 . TA T 138 PASSHow to...
View ArticleCanĀ“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 canĀ“t get the SNPs, I only get the Indels. I am working with a mutant I created from an E coli...
View ArticleIndel Annotation Tools, Not Loss Of Function
Hey,does anyone know one or more indel annotation tools, which are doing just the basic steps? Like: telling that an indel is laying on a splice site or on a mRNA region? I am not looking for all those...
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 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 ArticleNovel 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 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 ArticleWhat Kind Of Analysis Can Do You With Vcf Files?
What kinds of analyses can be completed if you have SNP, indel, and SV data in vcf files? I just need a few very broad and generic examples.
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 ArticleExtracting Two Bam Files And Indexing Them To Compare Indels
I need to fetch 2 BAM files from an HTTP server and I only need 'chr1' so I'm attempting to use:samtools view -h http://cdna.eva.mpg.de/denisova/alignments/T_hg19_1000g.bam chr1 chr1.bamfor each file...
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 ArticleWhat 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 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...
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