Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • GATK pipeline for SNP calling from 454 GS-FLX sequencing data????

    I want to call SNPs in GATK using the BAM file produced by GS Reference mapper , bu the problem with BAM file is it does not contain the read group so how to add read group in the bam file of 454 sequencing data and whether or not PICARD and GATK can be used to call SNPs from 454 sequencing data. Till now I was using samtools but now my task is to compare the output of Samtools and GATK. ANy help will be appreciated

  • #2
    Gatk2.0

    Originally posted by Maulik23 View Post
    I want to call SNPs in GATK using the BAM file produced by GS Reference mapper , bu the problem with BAM file is it does not contain the read group so how to add read group in the bam file of 454 sequencing data and whether or not PICARD and GATK can be used to call SNPs from 454 sequencing data. Till now I was using samtools but now my task is to compare the output of Samtools and GATK. ANy help will be appreciated
    The information you seek is out there in the help documentation. You will need to use Picard to add group information. I wrote a quick introduction to GATK2.0 here (http://gif.biotech.iastate.edu/blog/) I intend on following it up with my pipeline that i have created that takes in a same file and outputs a vcf file after going through bam conversion with samtooms, deduplication, sorting and read group addition with Picard and then GATK calling of SNPs. I have been using the new Haplotype caller which is slow unless you use it in parallel. The Queue system they have developed looks really powerful but I have had trouble implementing. I have found a work around and a way to load balance any genome for improved efficiency.

    I will work on the next post so it makes more sense.

    Comment


    • #3
      thanks for reply but my concern is with 454 sequencing data because I have not came across any good reference which has used GATK for SNP calling from Roche 454 sequencing data. Can you please brief me about the proper pipeline of SNP calling starting from adding of the read group to the variant calling in GATK using 454 sequencing data?

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM
      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 12:08 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      14 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      14 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      43 views
      0 likes
      Last Post seqadmin  
      Working...
      X