Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.

Which variant caller should be selected for my dataset?

NandaNanda CanadaMember

Hi,

I am currently working on two different projects and interested in finding common and rare variants.

Project1 -
Organism : Influenza virus
Number of samples : 18
Sequencing type: Exome sequencing
Alignment tool : BWA
Analysis ready BAM files :
- BAM files are generated using BWA,
- then sorted the bam
- deduplicated bam file using picard (markduplicates)
GATK variant caller : Unifiedgenotyper or HaplotypeCaller (Which one to be used?)

Project2 :
Organism : Human
Number of samples : 24
Sequencing type: DNAseq (paired-end)
Analysis ready BAM files :
- BAM files are generated using BWA,
- then sorted the bam
- and finally deduplicated and recalibrated_reads.bam
GATK variant caller : Unifiedgenotyper or HaplotypeCaller (Which one to be used?)

What is the criteria to select the variant caller?

Answers

Sign In or Register to comment.