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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

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