Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GATK SNP multi-sample without known SNP database ?

    I am working on identifying the SNPs in the genome of an insect which is sequenced in three samples. Following the GATK best practice pipeline i have completed the following task.

    Quality filtered reads.
    Read Alignment for each sample eg. S1, S2, S3.
    Sort and mark duplicates in each sample S1, S2, S3.
    Realign target and Indel realinger on each sample S1, S2, S3. Now i am stuck with next steps. As it require the base recalibration (BSQR) step. which require the known database of snps. however i dont have any known snp database so i am following the alternative steps mentioned the GATK for non-model organism. That is
    I call the raw SNPs in gvcf model from each sample and then make joint calling for a final combined vcf file.
    Next, I applied the hard filters on this file and extract good quality SNPs and indels as a reference database of BSQR step.

    Now the question is i have three realigned files S1_realigned.bam, S2_realigned.bam, S3_realigned.bam from step 4 and a reference database of SNP and Indels (if i am right) from the step 6. So how i would proceed further. Did i use against each sample separately or make a combine re-calibration table by providing all three in the same command.
    Thanks Dr. Deepak

Latest Articles

Collapse

  • 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
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X