Are there any tools or R packages for calculating the new amino acid chain, given an indel?
I've been asked to provide a set of putative...
50 results in 0.0024 seconds.
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Tool or package to convert new peptide sequence from frameshift variant?
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bowtie 2 dpad parameter explanation
Can someone provide a detailed explanation, what the bowtie2 parameter "--dpad" does? The explanation given in the manual is as follows: "--dpad... -
gold standard for human genome INDEL calling
Hi all!
I am evaluating the performance of our INDEL calling tool and comparing with others.I am using the INDELs dataset identified by Ryan Mills... -
A problem of using Samtools to make VCF file
Hi!
I used the samtools commands and 1000 genome data(phase 3, low-coverage sequenced data) to generate the VCF file for both snp and... -
Barcode splitter
Hello,
I am trying to use fastx barcode splitter, but I do not understand if with the option "partial matching " I can allow indel inside... -
gatk position indel
Hello,
I am implementing my pipeline for Roche 454 Junior and I have used GATK for called of variants.
I have compared my variants with Roche's...Last edited by pingu; 10-17-2015, 01:24 PM. -
Mapping SNPs to Chromosomes
I have a reference genome (.fa) and its annotation (.gtf) files. I have sequenced both DNA and RNA from test sample and generated vcf files containing... -
VCF Record Help
Can you combine vcf files and incorporate snps and indels that overlap on the same line/record?
Matt -
variant calling in plant
I am trying to get all variants of all types for a sequence I put together through an assembly step followed by consensus building using a reference.... -
Zygosity in Indel Calling
Hey, can anyone link me to any papers for indel callers that detail how they determine zygosity of the variant. Obviously for snps there are a number... -
tophat2 some parameters are not working (--no-novel-indels and -a)
I used tophat2 to map reads with --no-novel-indels and -a 6 parameters. Once the mapping is done, I examined the result (accepted_hits.bam) and found...Last edited by statsteam; 05-28-2014, 03:48 PM. Reason: putting a correct example for anchor length <6 -
Geneious - circular & iterative mapping, phased SNP variant effects, and more
We've made a short video demonstrating some of the cool things you can do in Geneious (http://www.geneious.com) that as far as we're aware either aren't... -
Homopolymer expansion variants
I'm interested to hear what kind of filtering people are using for homopolymer expansion variants, and what expectations are of the accuracy of those... -
How to handle heterozygous INDELS
Hey,
how do you handle INDELS which show in a .vcf file a heterozygous status. Meaning there are two alleles in the sample: 50% of the... -
NEWBIE: What is relation between SNP calling, INDEL calling and Genotype calling?
I know the snp is replace polymorphism and INDEL is about deletion or insertion. Are they relative to genotype calling, any stories? thx
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