Strelka Indel Allele Counts
Hopefully there are some Strelka users out there who can help with this one. I'm looking for allelic counts of the ref and non-ref allele of the indels.I see these flags in the VCF header, do these...
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 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 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 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 ArticleIndel Annotation Tools, Not Loss Of Function
Hey,does anyone know one or more indel annotation tools, which are doing just the basic steps? Like: telling that an indel is laying on a splice site or on a mRNA region? I am not looking for all those...
View ArticleNovel Sequence Insertions 1000 Genomes Project
I am looking for novel sequence insertions identified in the 1000 genomes project, and I found 3 files in this...
View ArticleHow 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 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 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 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 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 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 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 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 ArticleBWA Small Indels vs Roche Newbler Assembler
I've been experimenting with using BWA to assemble 454 (1kb reads), comparing previous assemblies performed with the proprietary Roche assembler and I've noticed that BWA seems to be able to handle...
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 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...
View ArticleCan´T Find The Snps With Samtools (Only Get Indels)
Hello everybody, Could anyone tell me how to get SNPs using SAMtools???. I am learning how to do it but can´t get the SNPs, I only get the Indels. I am working with a mutant I created from an E coli...
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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