Nanopolish variant calling --consensus number of variants in span (11) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes

[krishnakazama]

This is closely related to #501 but in my case, it is tick transcriptome I'm performing de novo assembly as I don't have a reference transcriptome. I'm confused about whether to consider this message or not(the number of variants in span (11) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes).

the script I have used. python3 ${nanopolish_makerange} ${assembly.fasta}
| parallel --results $nanopolish.results -P 7 ${thr}
nanopolish variants
--consensus
-o polished.{1}.vcf
-w {1}
-r ${basecalled.fasta}
-b ${reads.sorted.bam
-g ${assembly.fasta}
-t 4
--min-candidate-frequency=0.01

Ready to provide further details also Please do suggest some ideas

[jts]

It is just a warning that you can ignore. Nanopolish is not designed for transcriptome data so it is unlikely to work well for this case, sorry.

[jts]

You can ignore this warning. Also just a note but nanopolish isn’t designed for transcriptome polishing and I doubt it will work well.

On Aug 17, 2022, at 8:16 AM, krishnakazama @.***> wrote:

 This is closely related to #501 but in my case, it is tick transcriptome I'm performing de novo assembly as I don't have a reference transcriptome. I'm confused about whether to consider this message or not(the number of variants in span (11) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes).

the script I have used. python3 ${nanopolish_makerange} ${assembly.fasta} | parallel --results $nanopolish.results -P 7 ${thr} nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r ${basecalled.fasta} -b ${reads.sorted.bam -g ${assembly.fasta} -t 4 --min-candidate-frequency=0.01

Please do suggest some ideas

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