Question: Nanopore SNP and indels calling tool
gravatar for tarek.mohamed
10 months ago by
tarek.mohamed250 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 • 985 views
ADD COMMENTlink modified 5 months ago by WouterDeCoster39k • written 10 months ago by tarek.mohamed250

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 7 months ago by mohammadalkadi00

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 5 months ago by xunshengbu0
gravatar for WouterDeCoster
5 months ago by
WouterDeCoster39k wrote:

Tools worth mentioning for variant calling from nanopore data:

ADD COMMENTlink written 5 months ago by WouterDeCoster39k
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