How To Retrieve Reads Supporting A Snp/Indel
I used samtools and varscan for variant calling like this:samtools mpileup \ -f genome.fa \ tku.sorted.rmdup.bam \ | java -jar VarScan.v2.3.5.jar pileup2snp \ --min-coverage 8 \ --min-reads2 2 \...
View ArticleHow 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 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 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 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 ArticleProgramming Challange: Pairwise Alignments To Multiple Alignment
I have a set of 10-12 very closely related chromosome sequences (from different strains) aligned to a "single" reference chromosome. Now I need to generate multiple sequence alignment of these without...
View ArticleDetecting 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...
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 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 ArticleVcf Snps And Indels Mouse Genomes
Hi, I am using SNPs and INDELs data from the mouse genomes project and the data seem to have conflicting information. I mean, seems they report a SNP in a deleted position. Thus my question, Is it...
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 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 ArticleLarge Deletions With Bwa And Single End Reads
Hi, I am trying to detect deletions approximately 66bp in length by mapping 90 base reads to the human genome with BWA (and using GATK). By fine tuning the alignment parameters I have managed to...
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 ArticleAlternate 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...
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 ArticleIndel Discovery Delly, Pindel, Samtools, Gatk
I'm testing out samtools vs GATK for snp and indel calling, and looking at using pindel for SV in particular focusing on insertions and Delly for the other SV. What experience do people have of SNP...
View ArticleIndel Detection For 454 Resequencing
I do some work for a small diagnostics company that has a requirement for small indel detection in 454 data. Those of you familiar with Roche's pipeline will be aware that AVA (Amplicon Variant...
View ArticleReducing False Positive Indel Calls From Pindel
I am analyzing the specificity of Pindel's indel calls. I have matched tumor/normal WGS data, bwa aligned. The original calls were filtered to remove any that had supporting reads from the normal...
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...
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