Gatk3 Vs Dindel For Small Indel Calling
I read some posts from Heng Li around two years ago that he suggested Dindel is the optimal software for small indel calling. I'm just wondering if this is still true today because GATK seems to...
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? Â Most of the tutorials online involve starting from the...
View ArticleSimulating A Read With A Deletion Of 50 Bp Into It.
Im trying to test some indel calling programs with large deletions in sequencing reads. I ve got this sequence in Chromosome 20 of hg19 : > CTAGCAAGGG GGCTGTATGG CTTGAGGCCA TAGTCCAGGA CATCATCGGG...
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 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 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 ArticleSamtools Indels -- Filtering Only Hits With Insertion In The Reference In The...
Can anyone suggest how to use samtools to filter only hits where there is a insertion in the reference that splits the sequence hit roughly by the middle? My sequences are in the range of 100-1000bp...
View ArticleSearching For Deletion In A Low Number Of Reads
Hi everybody,I am having sort of a non-conform problem.we have a mutated mitochondrial genome (circular) of high coverage (~x10k). We know that there are a few deletions and insertions in there due to...
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 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 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 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 ArticleDeletions, 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 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 ArticleIs There A Convention For Representing Indels In Diploid Genome Sequences?
If an individual has a heterozygous indel how should that be represented in a sequence?I am looking for some examples along the lines ofA[C]GT or A[C/-]GT
View ArticleHow To Make A Circular Plot Of Snps And Indels ??
Hello everybody,I am analysing SNPs and INDELs in several prokaryotic genomes of the same strain. My goal is to compare them with a reference genome . I would like to learn how to plot the SNPs in a...
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 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 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...
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