Indel 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 ArticleHow To Call Snp And Indel Based On A Sanger Sequences Based Bac Contig Vs...
I have BAC contig, assembled from sanger sequences, that I want to use for quality control on my short read based SNP and indel call's.Which tool can I use to align the BAC sequence against the...
View ArticleSplit Vcf File Into Snps And Indels
Hi there,As recommended in the GATK best practices the Variant Quality Score Recalibration has to be done separately for SNPs and Indels. But, I didn't find the way to do this split in a clean way (for...
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 ArticleStructural 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...
View ArticleGenerate pileup for indels only using SAMtools mpileup
Is there a way to generate a pileup for indels only using the samtools mpileup command? The -I flag can be used to skip indel calling but there is no option to call indels only.Thanks.
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As of samtools 0.1.8 'mpileup' appears to have superseded 'pileup' for variant detection.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 ArticleSnps And Indels In Homozygous Genomes
I have a genomic sequence of an inbred mouse strain i.e. the genome is homozygous for a given position or same alleles are present on both of the strands. Now for variant calling, I have to compare it...
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 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 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 ArticleSamtools / Bcftools Missing Random Obvious Single Base Indels
I am using samtools to call variants in a haploid genome (yes I know it is designed for diploid). It finds SNPs easily, and most of the indels, but there are a few indels it can NOT seem to find no...
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 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 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 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 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 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 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 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 \...
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