How to call variants for mitochondrial genome data of nanopore minIon sequencing?

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6.4 years ago

pradyumna Jayaram ▴ 210

We tried to call variant using nanopolish but we need to specify the ploidy information, which is where we are stuck. can we give ploidy information as 1? When we give ploidy as 1 we got a warning saying

Number of variants in span (62) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!

[post-run summary] total reads: 2215, unparseable: 0, qc fail: 1, could not calibrate: 0, no alignment: 76, bad fast5: 0

Please guide me with this.

Thanks and regards

Pradyumna

genome SNP nanopore mitochondria nanopolish • 1.8k views

ADD COMMENT • link 6.4 years ago by pradyumna Jayaram ▴ 210

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How much coverage did you obtain? Did you try a pileup-based method for variant calling?

ADD REPLY • link 6.4 years ago by WouterDeCoster 48k

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No we didnot try any pileup based method, Please suggest what tools can be used for that(samtools mpileup?). We got ~400x coverage for the samples.

ADD REPLY • link 6.4 years ago by pradyumna Jayaram ▴ 210

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