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...
View ArticleIndel Notation In Variant Calling
HelloI am sorry for the basic question but I am struggling to find any details of the nomenclature of indels by variant calling software. Unfortunately i am unable to access the details of the software...
View ArticleMulti-Sample Indel Realignment Using Gatk
Is there a way to use the GATK Indel Realigner tool with a two-samples-input? The issue is that in my normal sample, several reads are mapped containing SNPs at specific positions, and ONE read having...
View ArticleHow Best To Add Custom Variation Track To Ucsc Browser?
I have generated sequence variants (SNPs/INDELs) by NGS resequencing and would like to display them on the UCSC browser (I have resequenced against a UCSC reference genome). Obviously i could use BED...
View ArticleBenchmarking Read Alignment And Variant-Calling Algorithms (For Dummies)
Hi all, I am wondering if there is a good step by step guide of how to benchmark alignment and variant calling software. I do understand the premise e.g.Generate reads with known mutations Align to...
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 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 ArticleHow 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...
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 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 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 ArticleBwa Indels
Comparing bwa 0.6.2 to bwa 0.5.9 I'm seeing very different behavior around indels. I'm using default options in both cases and as far as I can tell they haven't changed. I'm aligning Illumina paired...
View ArticleTrio: Detecting A Large De Novo Indel
I've been given a set of three BAM (father, mother, child) and I expect the child to contains some de-novo heterozygous variations . samtools mpileup have been used to find the small variations but...
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 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 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 To Set Filter For Frequency Of Reads And Hapmap Exome Sample Results:
Hey All, I only used so far three filters for my whole exome pipeline (aligning to hg19) for a HapMap sample. I tried it on the NA19240 Hapmap sample from paper below (Table 3) which shows ~196...
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 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 ArticleTool: Varscan: Variant Detection In Massively Parallel Sequencing Data
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, IonTorrent, Roche/454, and similar instruments. The newest...
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