Gatk3 Vs Dindel For Small Indel Calling
I read some posts from Heng Li around two years ago that he suggested Dindel is the optimal software for small indel calling. I'm just wondering if this is still true today because GATK seems to...
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 ArticleFiltering Vcf File
I was wondering how to filter the vcf file based on a few input arguments ( DP>10, MQ>30 and QD>20 or GT = "1/1" etc)? I m planning to use simple command on the command line to extract the...
View ArticleStructural Variation Detection On A Short Reads Simulation
Hi,I am trying to do the following exercise (still playing with indels):simulate short reads (and indels) out of a human genome chromosome,align the short reads simulated in (1),call indels using a SV...
View ArticleGenomic Alignment And Snp/Indel Calling - My First Ever "Pipeline"
So I have finally generated some reads and run it through what I guess could be called a very rudimentary 'pipeline'. I generated a million paired end reads with wgsim then aligned with bwa, and used...
View ArticleSomaticindeldetector Vs Unifiedgenotyper
Hey Guys, I've been establishing my own first pipeline for calling variants: Indels and SNPs. For that, I used mainly GATK tools. I'm doing this for whole genome and whole exome sequences of mouse...
View ArticleTool: Phylosim - Monte Carlo Simulation Of Sequence Evolution In The R...
PhyloSimPhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R. It is built on the top of the R.oo and ape packages and uses...
View ArticleSnps And Indels In Homozygous Genomes
I have a genomic sequence of an inbred mouse strain i.e. the genome is homozygous for a given position or same alleles are present on both of the strands. Now for variant calling, I have to compare it...
View ArticleWhat Is The Difference Between Samtools Mpileup And Pileup
As of samtools 0.1.8 'mpileup' appears to have superseded 'pileup' for variant detection. The samtools website now has pileup as deprecated. So i am wondering whether i should repeat my recent...
View ArticleInterpretation of InDels obtained from the Freebayes variant caller on...
Hello, I am calling variants on mitochondrial genomes using freebayes.Ā I am using the following command:Ā freebayesĀ -fĀ $REFĀ -pĀ 1Ā -FĀ 0.6Ā $BAMĀ |Ā $VCFFILTERĀ -fĀ "QUAL > 20"Ā >Ā $F_6_OUT I have been...
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 ArticleIndel Detection For 454 Resequencing
I do some work for a small diagnostics company that has a requirement for small indel detection in 454 data. Those of you familiar with Roche's pipeline will be aware that AVA (Amplicon Variant...
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 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 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 ArticleExtracting Specific Reads From Vcf File
Hello,I am trying to extract indels with coverage ~1 and they are in a VCF file. How do I write a python script or a shell commnad to extract those indels with coverage 1 only? This is the data:chr1...
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 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 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 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...
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