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?