Variant calling on Nanopore reads
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22 months ago
felix ▴ 20

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

genome alignment • 2.7k views
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22 months ago

I would suggest using Longshot.

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21 months ago
colindaven ★ 3.3k

Clair also has a good reputation in addition to Longshot https://www.biorxiv.org/content/10.1101/2020.02.07.939322v1?ct=

However I have found Longshot https://github.com/pjedge/longshot quite easy to install and run, as long as you can get over the initial RUST hurdles. Fascinatingly, it's the first tool I've seen which seems to be able to handle long reads' ability to actually (easily) phase SNVs.

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