Deletions, 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 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 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 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 Taking Forever! Help
Hi all, I am working on exome capture data for barley (1.3Gbp). I am interested in variant calling to find out SNPs in my sample. I have used SAMTools SNP calling and things get done in ~1 hr whereas...
View Article1000 Genomes Indel/Snps File
Is there any place to download 1000 genome SNPs and Indels data in a single merged file for each pilot (pilot 1 , 2 , and 3) ? I am trying to use GATK and thought to use 1KG indels and SNPs vcf files...
View ArticleWhat Are The Next Steps For Processing Indels From Gatk
Hi, I have raw calls for indels called using GATK, I wonder, where to start? filtering these calls? Should I plot the quality, depth etc. and then decide threshold to filter the bad calls? Any...
View ArticleMerging/Concatenating Vcf Files
I have a vcf file of SNPs and another vcf file for my Indels. During SNP calling step by GATK, I created them separately instead of using -glm (calling together SNPs and Indels). Now to get the...
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 ArticleSequence 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 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 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 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 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 ArticleSomaticindeldetector 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...
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...
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Indel Left/Right Alignment
When matching indels between different VCF files (generated by different callers), there is this issue with left / right indel alignment, For example: Here is a real example for one indel (from the...
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 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 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...
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