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 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 ArticleNgs Tool Analysis For Snp&Indel Calling Of Pooling Data
What are the best and most used analysis tool actually, for SNP and indel calling of pooled data?I'm using: GATK Freebayes that have specified options for data in pool.Now I have found CRISP.Are there...
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 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 ArticleReducing False Positive Indel Calls From Pindel
I am analyzing the specificity of Pindel's indel calls. I have matched tumor/normal WGS data, bwa aligned. The original calls were filtered to remove any that had supporting reads from the normal...
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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 ArticleStrelka Indel Allele Counts
Hopefully there are some Strelka users out there who can help with this one. I'm looking for allelic counts of the ref and non-ref allele of the indels.I see these flags in the VCF header, do these...
View ArticleWhole Genome Dna Amplification Before Applying Wgs
Dear allWe have some DNA samples that I would like to run whole genome sequencing on. Unfortunately these samples only contain very little DNA (too little for WGS). It has then been suggested to do...
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 ArticleHow To Set Filter For Frequency Of Reads And Hapmap Exome Sample Results:
Hey All, I only used so far three filters for my whole exome pipeline (aligning to hg19) for a HapMap sample. I tried it on the NA19240 Hapmap sample from paper below (Table 3) which shows ~196...
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 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 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 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 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 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 ArticleAnyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
I'm looking for a general variant annotator ... one that would call a variant as synonymous, non-synonymous, non-genic, UTR, frame-shift, truncation, etc. By general I mean that we should be able to...
View ArticleSplit Vcf File Into Snps And Indels
Hi there,As recommended in the GATK best practices the Variant Quality Score Recalibration has to be done separately for SNPs and Indels. But, I didn't find the way to do this split in a clean way (for...
View ArticleTool For Finding Indel In Which Part Of Genes
Are there any tools to help us determine whether an indel lies within a specific part of the gene ( Exon, Intron, ...)?
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