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How 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...

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Calculating 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...

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Does 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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Pindel 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...

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Comparing Genomic Assemblies To Find Indels

Hello everyone,We've sequenced a YAC containing a stretch of human DNA as an insert. We know what the insert sequence is supposed to be. However - as you could imagine - Illumina-based sequencing has...

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Comparative 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...

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Detecting Cancer Somatic Mutations From Multi-Sample Low-Pass Wgs Data

Hi All,Q1. I'm trying to find recurrent mutations (SNPs and indels) from multi-sample (~100) low-pass (3~4x) whole genome sequencing data for a certain cancer type. They are all paired with matched...

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Structural 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...

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Gatk3 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...

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Somaticindeldetector Vs Unifiedgenotyper

Hey Guys, I've been establishing my own first pipeline for calling variants: Indels and SNPs. For that, I used mainly GATK tools. I'm doing this for whole genome and whole exome sequences of mouse...

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Gatk 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...

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Alternate Sources Of Reference Indel Vcfs Outside Of Dbsnp And 1000 Genomes...

Hi,I am in a midst of testing some software tools for detecting indel from single sample genome data, and was wondering whether there is any source of reference indel files outside of dbSNP and 1000...

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Insertion 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??

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How To Call Variants (Snp, Indel, Sv) On A Bac Contig Aligned With Bwa Mem To...

I aligned a BAC contig (assembled from sanger sequences) to a reference genome using BWA-mem. The output alignments are very similar to the best end to end alignment I got from aligning the bac contig...

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Anyone 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...

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What 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...

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Simulating 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...

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What 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...

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How 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...

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Tools 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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