Nanopolish variant calling. Need to specify input region of the reference genome
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2.6 years ago
SUDOsundu ▴ 60

I mapped the reads with the reference fasta with minimap2. Out put: BAM file

Then I used the BAM, reference fasta, reads to nanopolish variant calling. And I got this error.

Error: genome has multiple contigs, please use -w to specify input region

My reference fasta contains 6 fasta sequences. It has no chromosome locations in it. Without knowing the chromosome locations (format: <chromsome_name>:<start>-<end>)) how do I specify the input region?

genome assembly • 831 views
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Entering edit mode
2.6 years ago

Chromosomes are irrelevant. The tool looks at contigs regardless of how well assembled these are, and considers every sequence in your reference fasta a contig.

Say that you have the following fasta file:

>my_fabulous_contig  
ATGCGCGCGC    
>and_another_contig  
GCTTACTTGTGTC

Then -w my_fabulous_contig:2-5 would be perfectly valid.

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