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generate “known_snps_unsorted.vcf” for a ref genome of different species or version #3

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bguo068 opened this issue Aug 17, 2022 · 1 comment
Open
1 of 2 tasks

generate “known_snps_unsorted.vcf” for a ref genome of different species or version #3

bguo068 opened this issue Aug 17, 2022 · 1 comment

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@bguo068
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bguo068 commented Aug 17, 2022 •
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Currently, we are using a version of the known_snps_unsorted.vcf file from Zalak, of which we don't know the source.

  • For pf, we may or may not need an updated version of known_snps_unsorted.vcf file
  • For pv, we have to update this file.
bguo068 added a commit that referenced this issue Dec 9, 2022
@bguo068
add prep_known_variant_vcf_pf
51a2f0b 
according to the [method document](http://ngs.sanger.ac.uk/production/malaria/pfcommunityproject/Pf6/Pf_6_extended_methods.pdf) of [MalariaGen Pfv6 paper](https://wellcomeopenresearch.org/articles/6-42) #3
bguo068 referenced this issue Dec 10, 2022
@bguo068
update scripts/description on preparing reference files (#7)
3fc4855 
1. scripts: ref/prep_ref_files.py
2. update params.known_sites to use PASS variants from pf crosses 1.0 vcf
3. update main Readme.md file to provide options to generate all ref file by users
4. update environment.yaml file to include requests package for downloading
@bguo068
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bguo068 commented May 26, 2023

Resources to find known sites for Pv:

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