Question: Variant calling on Nanopore reads
2
gravatar for felix
9 months ago by
felix20
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 • 913 views
ADD COMMENTlink modified 8 months ago by colindaven2.4k • written 9 months ago by felix20

Also see Nanopore SNP and indels calling tool

ADD REPLYlink written 9 months ago by ATpoint40k
3
gravatar for WouterDeCoster
9 months ago by
Belgium
WouterDeCoster44k wrote:

I would suggest using Longshot.

ADD COMMENTlink written 9 months ago by WouterDeCoster44k
1
gravatar for colindaven
8 months ago by
colindaven2.4k
Hannover Medical School
colindaven2.4k wrote:

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.

ADD COMMENTlink modified 4 months ago • written 8 months ago by colindaven2.4k
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