Hi I am working with Candida albicans genome for SNP calling. Its Whole genome data.
I used standard steps used here https://gencore.bio.nyu.edu/variant-calling-pipeline/
I am finding a very strange problem in my VCF file which i believe could be associated with HaplotypeCaller.
The SNP exist in the bam file but are not been called in vcf file.
I can also share my script and list interval file if that could help solving the problem.