Frequency Of Homozygous Indels Vs Heterozygous Indels
I have been surprised to read in Genetic Variation in an Individual Human Exome that most of indels in coding regions are homozygous:The HuRef genome contains a total of 739 coding indels, which...
View ArticleMerging Vcf Files And Filling In Missing Genotypes
I have vcf files with genomic variants (e.g. SNPs and Indels) from several patients. I now want to merge them into one vcf file e.g. using vcftools' merge-vcf. Doing that I get a file that holds for...
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 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 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 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 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 ArticleInterpretation of InDels obtained from the Freebayes variant caller on...
Hello, I am calling variants on mitochondrial genomes using freebayes. I am using the following command: freebayes -f $REF -p 1 -F 0.6 $BAM | $VCFFILTER -f "QUAL > 20" > $F_6_OUT I have been...
View ArticleHow To Call Variants (Snp, Indel, Sv) On A Bac Contig Aligned With Bwa Mem To...
I aligned a BAC contig (assembled from sanger sequences) to a reference genome using BWA-mem. The output alignments are very similar to the best end to end alignment I got from aligning the bac contig...
View ArticleWhat Do You Expect As The False Positive And Negative Rate For Snp'S And...
What do you expect as the false positive and negative rate for SNP's and INDELS in a WGS experiment?On which papers and data sets (inhouse or external) do you base this? Edit: Of course this depends on...
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 ArticleSNP and In/Del Counting without Raw Sequence Data
Is there an easy way to do SNP calling on multiple sequences of a gene (from different members in a population) without the raw sequence data? Most of the tutorials online involve starting from the...
View ArticleHow Are Indel Coded In Vcf Files
Hello,I have a question concerning how are INDEL coded in VCF files. I have for instance the following file:CHROM POS ID REF ALT QUAL FILTER8 18078835 . TTA T 46 PASS8 18078836 . TA T 138 PASSHow to...
View ArticleTools For Large Indels Discovery In Single-End Rna-Seq Reads
Hi all,Has anyone heard about any tool wich could deal with large indels discovery? I've found some for paired-end reads but never for single-end... My final goal is to find transposable elements...
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 ArticleIs there any way to quantify differences between neighbour-joining...
I am working on a project and I am currently only using the SNP data to make my trees. I would like to compare the trees made using SNP data to the trees made using indel data to ensure they are...
View ArticleHow Many Is Too Many? Germline And Somatic Coding Indels And Snps In Cancer...
Would anyone care to share their experience with variant calling in cancer genomics using tumor - normal pair to find somatic vs germline variants especially indels?I have been getting an unbelievably...
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 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 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...
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