Functional 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 ArticleGatk Indel Realignment Taking Forever! Help
Hi all, I am working on exome capture data for barley (1.3Gbp). I am interested in variant calling to find out SNPs in my sample. I have used SAMTools SNP calling and things get done in ~1 hr whereas...
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...
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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 ArticleHow to call low frequency snp/indel with GATK's HC/UG
i want to call snp/indel with low frequency, like DP=100, ALT=10.how to set HC/UG ?with UG, i run with :--min_indel_count_for_genotyping 2--min_indel_fraction_per_sample 0.05get a nice result, but i...
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 ArticleWhat Is Difference Between Gatk And Dindel For Calling Indel
What is difference between GATK and Dindel for calling indel ,I see that in the GATK second step :discovery indel ,The genotype likelihoods calculation is inspired by Dindel.So I want to know the...
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 ArticleWhat Approach Would You Recommend For Large Indel Detection With Solid Data
I've been spending quite some time on following problem: I sequenced a bacterial genome using paired-end reads (SOLiD) and I have a quite good reference sequence. My goal is to detect changes in the...
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, ...)?
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 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 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 ArticleWhat Do You Do With Indels Data?
I have a list of insertion and deletion from a whole genome sequence obtained by next generation sequencer, chr, pos and sequence for each indels aligned to our reference genome.I'm not familiar with...
View ArticleHow To Transform Adjacent Complex Variants In Vcf Format To Individuals'...
Hello, everyone. Recently, I have downloaded the latest variant data of 1000genomes project from ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20110521/ and the mapped data from...
View ArticleGatk Threshold Parameter For Clipping Of Reads During Indel Calling Running...
GATK 1.6 claims to apply a Q20 threshold to clip ends of the reads for the indel caller:http://www.broadinstitute.org/gatk/guide/article?id=12373. Indel Calling with the Unified Genotyper [...] while...
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 ArticleDoes Anyone Know Of A Publication Reviewing Snp/Indel Finding Algorithms For...
Hi all, Is anyone aware of a good publication that reviews current methods for detecting SNPs/Indels from next gen sequencing data? I have done some searching but so far in vain. It would be great to...
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 ArticleIndel and missing in mach phased output
In mach phased output, how does it represent missing genotypes and indels?
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