Simulating 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 ArticleWhat Kind Of Analysis Can Do You With Vcf Files?
What kinds of analyses can be completed if you have SNP, indel, and SV data in vcf files? I just need a few very broad and generic examples.
View ArticleComparing Genomic Assemblies To Find Indels
Hello everyone,We've sequenced a YAC containing a stretch of human DNA as an insert. We know what the insert sequence is supposed to be. However - as you could imagine - Illumina-based sequencing has...
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 ArticleFrequency 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 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As of samtools 0.1.8 'mpileup' appears to have superseded 'pileup' for variant detection.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 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 ArticleComparative Genomic Analysis Of Bacterial Field Strains
Hi, I have a question on comparative genomics of bacterial field strains.If there is a very low number (only 30) of variants (base substitutions, indels etc) in a comparative genomics study of several...
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 ArticleVcf Snps And Indels Mouse Genomes
Hi, I am using SNPs and INDELs data from the mouse genomes project and the data seem to have conflicting information. I mean, seems they report a SNP in a deleted position. Thus my question, Is it...
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 Does Left-Alignment Work For Indels? Does It Address All Complicated...
I can vaguely guess its meaning but want to know, at least, how it works in different situations. Besides, after left alignment, can we write an indel in VCF file in a unique way?Thank you!
View ArticleUnknown Indel Notation To Hgvs
I'm sorry about this caotic question, but I don't understand nothing at all... I have a file of Indels finded in genes, presumably from HGMD. Well, i don't know how to read this file, i don't have any...
View ArticleIs It Possible To Get Rs Numbers For Indels?
I am currently designing an Illumina custom GoldenGate platform (for the first time, so with lack of experience..). I have finished the selection of SNPs and I'm ready to submit the list for...
View ArticleWhat Is The Best Tool For Mouse (Mm9 Or Mm10) Variant Annotations?
I am working with some mouse exome capture data, and I would like to provide functional annotations to variants (SNPs and small indels).For human data, I would typically use ANNOVAR. It looks like...
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 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 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 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 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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