Reference of Whole exome sequecing analysis · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Reference of Whole exome sequecing analysis

Dear all

I am new for WES analysis and want to ask which human reference genome should i download for Whole Exome analysis. Please share a direct link to the genome assembly and also the gtf/gff3 file if it should be used. It is very confusing with so many variants of human genome i.e masked, unmasked, alt, rm, toplevel etc.

Best Regards Shahzad

wes ngs variant calling mutation bwa

• 1,523 views • link

updated 6.4 years ago by lakhujanivijay

• written 6.4 years ago by Shahzad •

1 answer

I prefer downloading from iGenomes

This link should have pre-indexed genome files that you require

• 0 views • link

written 6.4 years ago by lakhujanivijay

Log in to answer this question.

More posts like this

Isaac aligner V4 genome aligner questions
written 2.8 years ago by DJBill •

1) For the alignment of the human whole exome sequence FASTq data to the human GRCh38p14 reference genome, and using the Isaac aligner V4, do …
Blog: WGS vs WES: Which Genetic Sequencing Method is Right for You?
written 3.4 years ago by Novogene •

Whole genome sequencing (WGS) and whole exome sequencing (WES) are two of the most popular methods used in modern genetic research. While both methods provide …
How to transform a whole-genome callset into whole-exome callset?
written 4.9 years ago by Alejandro Rojo •

Hi all, I have a callset from whole-genome data and with this callset, I want to transform it into exome callset by extracting the variants …
detection of single nucleotide variations with RNA-seq
written 5.7 years ago by mlemusfuentes •

hello everyone, I need know if someone has performance detection of single nucleotide variants (SNVs) using RNA-seq data. I know that the gold standard method …
Which types of human reference genome should be used for VCF normalization
written 6.7 years ago by seta

Dear all, I have got multiple single sample vcf files that should be merged into multi-sample vcf file. For the VCF normalization step before doing …
How many variants shall I expect in .vcf file?
written 8.8 years ago by Adam •

**Dear Biologists and Bio-IT-specialists,** based on your knoweledge and experience I'd like to know how many variants should be discovered from .BAM file (final result, …
Powerful desktop computer for genomics
written 10.2 years ago by Alternative

Dear all, I would like to purchase a desktop computer to be used by a student to run NGS pipelines for whole genome exome sequencing, …
RNA Seq for Dementia
written 11.9 years ago by ps1212 •

What are the questions that I should be asking when I do RNA-Seq trascriptome analysis of Alzheimers? I also have Exome data and Whole genome …
Tophat2 Error With Repeat-Masked Genome!!
written 12.7 years ago by Rahul Sharma

<p>Dear all,</p> <p>I was trying to <strong>map</strong> the <strong>RNA seq data</strong> on the <strong>assembled genome</strong>. I was using Tophat <code>tophat-2.0.10.Linux_x86_64</code> and Bowtie2 <code>bowtie2-2.1.0</code>. When I …
Chr_Random Positions
written 15.3 years ago by Biomed

<p>The sequencing center we work with recently started to report variants for random chromosomes, we now end up with variants (whole exome) that have been …