Could this pipeline run with assembled genome file only? without the reads file.

starskyzheng / panpop

Application of pan-genome for population

MIT License

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Could this pipeline run with assembled genome file only? without the reads file. #33

Closed kmosi0 closed 7 months ago

kmosi0 commented 7 months ago

I have the many assembled genome file, without the reads file. Could this pipeline support assembled genome file only? Thank you!

starskyzheng commented 7 months ago

Sorry. PanPop pipeline Not support this yet. You can use run_PART.pl to combine vcfs generated by svim-asm. Noted a pre-process is needed: perl scripts/long_caller_parser.pl --in {input.vcf} --out - --out_inv {output.inv_bed} --ref {input.ref} 2>>{log} | {BCFTOOLS} sort -O z -o {output.vcf}

kmosi0 commented 7 months ago

OK, thank you very much!