Large 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 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 ArticleHow To Identify/Flag The Presence Of Indels On The Read Level Nearby A Given...
Let's say I have list of genomic positions, e.g. SNP calls in a VCF file, and a BAM file with read alignments. What would be the best way to, for each of those positions, determine if in the BAM file...
View ArticleNovel Sequence Insertions 1000 Genomes Project
I am looking for novel sequence insertions identified in the 1000 genomes project, and I found 3 files in this...
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 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 ArticleGatk Indel Realignment Error - Mismatch In Index Files And Dict File
Greetings,I am aligning pooled sequencing data to a new renferece genome. GATK won't generate intervals because not every scaffold in the reference is found in my bam index?What am I missing? It seems...
View ArticleBwa Aln For Snp/Indel Discovery With Paired End 100Bp Human Dna Reads
Hi, Can anyone show me a recommended command line input to achieve this? I have never used the program before and am afraid of entering inappropriate values for one of the many paramters.Or is there a...
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 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 ArticleDifferences Running Dindel On Different Unix Environments
Hi all, I am hoping to try out dindel for indel-calling on my NGS data but coming up against some problems getting it to work on both institute's computing cluster and my desktop machine. On the...
View ArticleFrequency Of Homozygous Indels Vs Heterozygous Indels
I have been surprised to read in Genetic Variation in an Individual Human Exome that most of indels in coding regions are homozygous:The HuRef genome contains a total of 739 coding indels, which...
View ArticleHow To Calculate Genotype Concordance Between Indel Call Sets?
How do people calculate genotype concordance between INDEL call sets? I have a NGS and BAC based INDEL call set (in vcf) but I get a higher false positive and false negative rate than mentioned in some...
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 ArticleHow Best To Add Custom Variation Track To Ucsc Browser?
I have generated sequence variants (SNPs/INDELs) by NGS resequencing and would like to display them on the UCSC browser (I have resequenced against a UCSC reference genome). Obviously i could use BED...
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 Do You Do Local Realignment Around Indels For Exome Sequencing?
Hi all, I am wondering how people generally go about local realignment around indels in their workflow? The most popular programs seem to be SRMA and GATK - does anyone use anything else?In my initial...
View ArticleWhat Are The Next Steps For Processing Indels From Gatk
Hi, I have raw calls for indels called using GATK, I wonder, where to start? filtering these calls? Should I plot the quality, depth etc. and then decide threshold to filter the bad calls? Any...
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 ArticleHow To Make A Circular Plot Of Snps And Indels ??
Hello everybody,I am analysing SNPs and INDELs in several prokaryotic genomes of the same strain. My goal is to compare them with a reference genome . I would like to learn how to plot the SNPs in a...
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