Question: Nanopore SNP and indels calling tool
gravatar for tarek.mohamed
18 months ago by
tarek.mohamed260 wrote:

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

nanopore calling tools indels snps • 2.0k views
ADD COMMENTlink modified 14 months ago by WouterDeCoster42k • written 18 months ago by tarek.mohamed260

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

ADD REPLYlink written 16 months ago by mohammadalkadi010

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.

ADD REPLYlink written 14 months ago by xunshengbu0
gravatar for WouterDeCoster
14 months ago by
WouterDeCoster42k wrote:

Tools worth mentioning for variant calling from nanopore data:

ADD COMMENTlink written 14 months ago by WouterDeCoster42k
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