since alleles contain undefined nucleotides

eblerjana / pangenie

Pangenome-based genome inference

MIT License

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since alleles contain undefined nucleotides #72

Open jwli-code opened 7 months ago

jwli-code commented 7 months ago

singularity exec ~/software/pangenie/container/pangenie.sif PanGenie-index -v keepA_C_0.5missing_100kbub_phased_deleteN_id_trim_filtered_SVs.vcf -r ZS11.genome.fa -t 24 -o PanGenie

My vcf sequence contains sequences with bases N, and I get an error when building index.

eblerjana commented 7 months ago

PanGenie skips variants with missing sequence information, since it is based on kmers. However, it should just give a warning instead of an error and proceed running. Can you please provide more details?