How 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 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 ArticleWhole Genome Dna Amplification Before Applying Wgs
Dear allWe have some DNA samples that I would like to run whole genome sequencing on. Unfortunately these samples only contain very little DNA (too little for WGS). It has then been suggested to do...
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 ArticleGenerate pileup for indels only using SAMtools mpileup
Is there a way to generate a pileup for indels only using the samtools mpileup command? The -I flag can be used to skip indel calling but there is no option to call indels only.Thanks.
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 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 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 ArticleFunctional Consequence of In-frame Indel
Does anybody include in-frame indels in association studies? A quick pubmed / google / biostars search on this didn't come up with much. In-frame indels are often treated as synonymous, but since they...
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 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 ArticleStrange variant call it show a indel but looks like a SNP
Hello all, i have a variant from a ION PGM sequencing, called with the ION Torrent variant caller plugin CHR POS ID REF ALT chr22 44324726 . T TG The flow cell...
View ArticleArlequin Input Frequency Data
Hi!I have frequency data for 50 biallelic loci and 500 samples in 3 populations and i can´t understand how to create an input file for arlequin with these data. If someone could help me it will be...
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 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 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...
View ArticleChip-Seq Peak Caller Able To Find Peaks Split By Indels?
Are there any chip-seq peak callers able to find cases where the region under a peak has been split by an indel between the reference and the chipped sample?For example, let's suppose one has done...
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 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 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...
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