Answers.Body: <p><a href="https://github.com/USDA-VS/vSNP" rel="nofollow noreferrer">vSNP</a> can be used to target specific regions of a genome. Pipeline is a 2 step process:</p>
  
  <ol>
  <li>create VCF files (via Freebayes)</li>
  <li>then in your case run all 100 VCF files to create SNP table</li>
  </ol>
  
  <p>A filter file can be supplied to step 2.  By filtering all position ranges other than the genes of interest, step 2 will output a SNP table (.xlsx) with only your genes of interest.  Also, table will include annotation if GBK is provide. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-13T20:11:27.487Z
Answers.LastActivityDate: 2020-02-13T20:11:27.487Z
Answers.UserDisplayName: Stuber
Body: <p>I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone tell me what snp analysis pipeline is best for targeted variation and not whole genome?
  I have this in mind:
  Mapping the reads with bwa and then using varscan
  Hope to hear for more options</p>
  
Tags: <snp><variant-calling><bwa><wgs>
Title: Variant calling for a subset of genes using whole gneome sequencing data
ThreadText: # Variant calling for a subset of genes using whole gneome sequencing data
  
  (Asked by: username_0 on 2020-02-12)
  
  I have few 100 raw fastq files from whole-genome sequencing data and I would like to map these files to a set of genes only (and not whole genome) so as to find SNP's associated with them. Can anyone tell me what snp analysis pipeline is best for targeted variation and not whole genome?
  I have this in mind:
  Mapping the reads with bwa and then using varscan
  Hope to hear for more options
  
  **Tags:** snp, variant-calling, bwa, wgs
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-02-13. Score: 0
  
  [vSNP](https://github.com/USDA-VS/vSNP) can be used to target specific regions of a genome. Pipeline is a 2 step process:
  
  1. create VCF files (via Freebayes)
  2. then in your case run all 100 VCF files to create SNP table
  
  A filter file can be supplied to step 2. By filtering all position ranges other than the genes of interest, step 2 will output a SNP table (.xlsx) with only your genes of interest. Also, table will include annotation if GBK is provide.
  
  
  ---
  
  