Arlequin Input Frequency Data
Hi!I have frequency data for 50 biallelic loci and 500 samples in 3 populations and i can´t understand how to create an input file for arlequin with these data. If someone could help me it will be...
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 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 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 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 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 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 ArticleSamtools: Local Realignment Around Indel
In samtools mpileup, adjust the option -m and -F to control when want to initiate indel realignment, any guideline to set the values for m and F for high coverage data (eg. >=20X)low coverage data...
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 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 ArticleIndel Annotation Tools, Not Loss Of Function
Hey,does anyone know one or more indel annotation tools, which are doing just the basic steps? Like: telling that an indel is laying on a splice site or on a mRNA region? I am not looking for all those...
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 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 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 ArticleIndel Discovery Delly, Pindel, Samtools, Gatk
I'm testing out samtools vs GATK for snp and indel calling, and looking at using pindel for SV in particular focusing on insertions and Delly for the other SV. What experience do people have of SNP...
View ArticleHow To Detect Overlaping Indels In Vcf File?
Hi all,I have a vcf file with indels from a whole genome analysis and I want to detect overlapping between indels... I tried to use BEDtools-intersect but it asks for 2 files, and I only have a single...
View ArticleNext Gen Sequencing Indel Realignment With The Genome Analysis Toolkit (Gatk)
As I continue to add steps to my SNP/Indel discovery workflow, the latest recommendation is local realignment around Indels using GATK following the initial alignment step. I have just commenced the...
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 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 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 Article