Anyone 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 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 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 ArticleComparative Genomic Analysis Of Bacterial Field Strains
Hi, I have a question on comparative genomics of bacterial field strains.If there is a very low number (only 30) of variants (base substitutions, indels etc) in a comparative genomics study of several...
View ArticleCanĀ“T Find The Snps With Samtools (Only Get Indels)
Hello everybody, Could anyone tell me how to get SNPs using SAMtools???. I am learning how to do it but canĀ“t get the SNPs, I only get the Indels. I am working with a mutant I created from an E coli...
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 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 ArticleGatk3 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 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 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...
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 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 ArticleMerging Vcf Files And Filling In Missing Genotypes
I have vcf files with genomic variants (e.g. SNPs and Indels) from several patients. I now want to merge them into one vcf file e.g. using vcftools' merge-vcf. Doing that I get a file that holds for...
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 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 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 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 ArticleClassify Mutations Which Are Found Ny Using Exome Sequencing
Hi, everyone. I used exome sequencing to sequence tumor and blood, and after I remove mutations in blood and snp in dbsnp131, I found I still have about 2000 mutations. I read the exome sequencing...
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...
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