What 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 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...
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 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 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 ArticleProgramming Challange: Pairwise Alignments To Multiple Alignment
I have a set of 10-12 very closely related chromosome sequences (from different strains) aligned to a "single" reference chromosome. Now I need to generate multiple sequence alignment of these without...
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 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 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 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 Handle Reads Ending With Deletions In Gatk?
Hello,before asking my question, I should point out that I'm working with data that's not my own (publicly available), to learn and establish a proper workflow when real data wlll arrive in the...
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 ArticleClik here to view.
Indel Left/Right Alignment
When matching indels between different VCF files (generated by different callers), there is this issue with left / right indel alignment, For example: Here is a real example for one indel (from the...
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 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 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 ArticleFunctional Consequence of In-frame Indel
Does anybody include in-frame indels in association studies? A quick pubmed / google / biostars search on this didn't come up with much. In-frame indels are often treated as synonymous, but since they...
View ArticleLocating Indels In Gene
I have a excel file from windows (spreadsheet) contains start, end and indel sequences (-GGC means GGC deletion or +AAC means AAC insertion) in column 1, 2 and 3 respectively. I have a reference genome...
View Article