Does Haplotypecaller of GATK find all the mutations?

Question

[Researcher]

Hi, I have some assembled sequences and know that some genes with specific mutations are present in them. However, when I go from fatsq to bam format and then apply haplotypecaller of GATK tool, very few of these genes are missing. So, I was wondering whether these genes and their variants did not appear because of applying haplotypecaller of GATK tool or because of the earlier stages from the fastq format to bam file? Thanks

Answer 1

[igor]

If you think your variant caller is not producing the expected output, you can manually examine your BAM in a genome browser like IGV. That will help explain why a particular locus is or is not reported as a variant.