If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Identifying good SNPs

I start working with IGV, but I have some doubts in how to identify a good SPN in this program.
First I download the new Soybean Genome on Phytozome (Gmax_275_v2.0.fa and Gmax_275_Wm82.a2.v1.gene.gff3 files), and then I upload my files (sample.vcf, sample.bam and sample.bam.bai) into the program. I indexed which files that program needed, so that's OK!
But my doubt is which parameters should I consider for a good SNP? For example, what I need to see on Alleles, Genotypes and Variant Attributes? See the example below.

Chr: Chr06
Position: 35170948
ID: .
Reference: C*
Alternate: T
Qual: 160
Type: SNP
Is Filtered Out: No

No Call: 0
Allele Num: 2
Allele Count: 4
Allele Frequency: 1

Minor Allele Fraction: 1

Non Variant: 0

  • No Call: 0
  • Hom Ref: 0
    Variant: 1

  • Het: 0

  • Hom Var: 1

Variant Attributes
AF1: 1
RPB: 5.557190e-01
VDB: 1.587578e-01
Depth: 18
FQ: -54
DP4: [1, 1, 6, 8]
AC1: 2
Mapping Quality: 25
PV4: [1, 0.22, 1, 0.24]



Sign In or Register to comment.