GATK 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 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 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 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 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 ArticleDo you guys have any recommendation on variant calling using long contigs or...
I have assembled a human genome and used bwa mem aligning the contigs back to the reference genome. Do you guys have any recommendation of variant caller?
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 ArticleHow to retrieve reads supporting a SNP/indel
I used samtools and varscan for variant calling like this:samtools mpileup \ -f genome.fa \ tku.sorted.rmdup.bam \ | java -jar VarScan.v2.3.5.jar pileup2snp \ --min-coverage 8 \ --min-reads2 2 \...
View ArticleArlequin Input Frequency Data
Hi!I have frequency data for 50 biallelic loci and 500 samples in 3 populations and i canĀ“t understand how to create an input file for arlequin with these data. If someone could help me it will be...
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 ArticleDo You Guys Have Any Recommendation On Variant Calling Using Long Contigs Or...
I have assembled a human genome and used bwa mem aligning the contigs back to the reference genome. Do you guys have any recommendation of variant caller?
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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 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 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 ArticleArlequin Input Frequency Data
Hi!I have frequency data for 50 biallelic loci and 500 samples in 3 populations and i canĀ“t understand how to create an input file for arlequin with these data. If someone could help me it will be...
View ArticleWhat Do You Expect As The False Positive And Negative Rate For Snp'S And...
What do you expect as the false positive and negative rate for SNP's and INDELS in a WGS experiment?On which papers and data sets (inhouse or external) do you base this? Edit: Of course this depends on...
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 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 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 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...
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