Question: Variant calling on Nanopore reads
gravatar for felix
3 days ago by
felix20 wrote:

I am currently working on nanopore reads, and trying to calculate the SNP and Indel count. I mapped the reads with Minimap2. From here I called the variants with GATK.

I know that GATK is actually written for short Illumina reads, so I was wondering if the results from the variant calling are trustworthy and whether there is a tool which is specialized on calling variants based on nanopore reads.

Thank you for your help

alignment genome • 82 views
ADD COMMENTlink modified 3 days ago by WouterDeCoster42k • written 3 days ago by felix20

Also see Nanopore SNP and indels calling tool

ADD REPLYlink written 3 days ago by ATpoint28k
gravatar for WouterDeCoster
3 days ago by
WouterDeCoster42k wrote:

I would suggest using Longshot.

ADD COMMENTlink written 3 days ago by WouterDeCoster42k
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