Nanopore SNP and indels calling tool

Question

[tarek.mohamed]

Hi,

I am working with sequencing data generated by minion. I used minimap2 to align the long reads to reference human genome GRCh38. Now I want to call SNPs and indels, I have been searching for a tool that can work with bam files generated by minimap2.

1. Is there variant caller that work with fastq files (not fast5) and can work with bam files generated by different aligner?
2. Why do the majority of variant calling tools (for nanopore) require bam files that are generated by specific aligner?

Thanks
Tarek

[MohammadAlkadi]

I don't think nanopore is suitable for SNPs and indels. Maybe this is the reason why you won't find tools!

[xunshengbu]

SNPs calling requires very high depth from reads with high quality, which both are challenges to Nano. Now it's possible to get high coverage NanoPore data, but not sure if anyone has estimated what's the minimum depth for NanoPore reads to call SNPs.

Answer 1

[WouterDeCoster]

Tools worth mentioning for variant calling from nanopore data:

• https://github.com/aquaskyline/Clairvoyante
• https://github.com/jts/nanopolish