How can I get the number of reads per variant in hisat2?

Question

[Nemo]

Hello,

I would like to see how many reads I have per variant. Is there any way to get this information using hisat2 or gatk or any other tool?

[ATpoint]

It's called variant calling. The VCF contains that information. Given your post history it seems you are essentially going blind in your project. I suggest to search for some guided tutorials to get started. The Biostars Handbook would be one option, but it's not entirely free though.

[Nemo]

Thanks @ATpoint I have already the variants (vcf format) using gatk haplotypecaller. But I do not see such information like reads per variant in the resulted output file (I see depth of reads and so on but not number of reads per variant). I also looked into biostar handbook the Variant Calling section, and I couldnt find any information related to this.

[Arup Ghosh]

Number of reads supporting REF & ALT allele: https://gatk.broadinstitute.org/hc/en-us/articles/360037052092-StrandBiasBySample