What 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 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 ArticleIs There A Convention For Representing Indels In Diploid Genome Sequences?
If an individual has a heterozygous indel how should that be represented in a sequence?I am looking for some examples along the lines ofA[C]GT or A[C/-]GT
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 ArticleExtracting Two Bam Files And Indexing Them To Compare Indels
I need to fetch 2 BAM files from an HTTP server and I only need 'chr1' so I'm attempting to use:samtools view -h http://cdna.eva.mpg.de/denisova/alignments/T_hg19_1000g.bam chr1 chr1.bamfor each file...
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 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 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 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 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 ArticleIndel Notation In Variant Calling
HelloI am sorry for the basic question but I am struggling to find any details of the nomenclature of indels by variant calling software. Unfortunately i am unable to access the details of the software...
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 ArticleLarge Deletions With Bwa And Single End Reads
Hi, I am trying to detect deletions approximately 66bp in length by mapping 90 base reads to the human genome with BWA (and using GATK). By fine tuning the alignment parameters I have managed to...
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 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 ArticleDeletions, Translocations And Cnv From Rna-Seq
Is it possible to find out deletions tarnslocations and / or copy number variations between RNA-seq data of control vs treated samples. The data is PE with enough coverage ( say around 30X).Thanks
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: Varscan: Variant Detection In Massively Parallel Sequencing Data
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, IonTorrent, Roche/454, and similar instruments. The newest...
View Article1000 Genomes Indel/Snps File
Is there any place to download 1000 genome SNPs and Indels data in a single merged file for each pilot (pilot 1 , 2 , and 3) ? I am trying to use GATK and thought to use 1KG indels and SNPs vcf files...
View ArticleMerging/Concatenating Vcf Files
I have a vcf file of SNPs and another vcf file for my Indels. During SNP calling step by GATK, I created them separately instead of using -glm (calling together SNPs and Indels). Now to get the...
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