How To Identify/Flag The Presence Of Indels On The Read Level Nearby A Given...
Let's say I have list of genomic positions, e.g. SNP calls in a VCF file, and a BAM file with read alignments. What would be the best way to, for each of those positions, determine if in the BAM file...
View ArticleLocating Indels In Gene
I have a excel file from windows (spreadsheet) contains start, end and indel sequences (-GGC means GGC deletion or +AAC means AAC insertion) in column 1, 2 and 3 respectively. I have a reference genome...
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 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 ArticleGatk Indel Realignment Dies In A Memory Explosion... Any Fixes?
I got the following rather strange error while running GATK indel realignment on a considerably larger file (HiSeq) than I am used to:Exception in thread "main" java.lang.OutOfMemoryError: GC overhead...
View ArticlePindel Error: Shiftedvector Out-Of-Range Error
Hello,I’ve been running pindel like so: pindel --config-file bam_config.txt --fasta /path/to/hg19/fasta/ --chromosome ALL --output-prefix /path/to/outputand I’ve noticed a lot of my pindel jobs fail...
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 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 ArticleComparative Genomic Analysis Of Bacterial Field Strains
Hi, I have a question on comparative genomics of bacterial field strains.If there is a very low number (only 30) of variants (base substitutions, indels etc) in a comparative genomics study of several...
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 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 ArticleWhat Do You Expect As The False Positive And Negative Rate For Snp'S And...
What do you expect as the false positive and negative rate for SNP's and INDELS in a WGS experiment?On which papers and data sets (inhouse or external) do you base this? Edit: Of course this depends on...
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 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 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 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 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 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 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 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...
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