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