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

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2.3 years ago

Nemo • 0

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?

alignemnt variant gatk covid hisat2 • 689 views

ADD COMMENT • link updated 2.3 years ago by Arup Ghosh 3.2k • written 2.3 years ago by Nemo • 0

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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.

ADD REPLY • link 2.3 years ago by ATpoint 85k

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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.

ADD REPLY • link 2.3 years ago by Nemo • 0

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

ADD REPLY • link 2.3 years ago by Arup Ghosh 3.2k

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