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Script to generate template VCF file for assembly #166

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timothymillar opened this issue Jul 11, 2023 · 2 comments
Closed

Script to generate template VCF file for assembly #166

timothymillar opened this issue Jul 11, 2023 · 2 comments
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enhancement New feature or request
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v0.9.0

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Simple script to generate a template VCF for MCHap assemble.

There are several motivations for this:

  • Simplicity, we only need position and alleles of putative segregating sites
  • Speed, less compute and using same input files
  • Ability to mask reference allele to lower parameter space Allow masking of SNV reference alleles #165
@timothymillar timothymillar added the enhancement New feature or request label Jul 11, 2023
@timothymillar timothymillar self-assigned this Jul 11, 2023
@timothymillar timothymillar added this to the v0.9.0 milestone Jul 11, 2023
timothymillar added a commit to timothymillar/MCHap that referenced this issue Jul 12, 2023
@timothymillar
Initial implimentation of basis-snvs tool PlantandFoodResearch#166
38de67b
timothymillar added a commit to timothymillar/MCHap that referenced this issue Jul 12, 2023
@timothymillar
Initial implimentation of basis-snvs tool PlantandFoodResearch#166
72e8aeb
timothymillar added a commit to timothymillar/MCHap that referenced this issue Jul 12, 2023
@timothymillar
Initial implimentation of basis-snvs tool PlantandFoodResearch#166
f2fd201
timothymillar added a commit to timothymillar/MCHap that referenced this issue Jul 12, 2023
@timothymillar
Initial implimentation of find-snvs tool PlantandFoodResearch#166
7ad6f53
timothymillar added a commit to timothymillar/MCHap that referenced this issue Jul 12, 2023
@timothymillar
Initial implimentation of find-snvs tool PlantandFoodResearch#166
cc51352
timothymillar added a commit to timothymillar/MCHap that referenced this issue Jul 13, 2023
@timothymillar
Initial implimentation of find-snvs tool PlantandFoodResearch#166
2b616a1
timothymillar added a commit to timothymillar/MCHap that referenced this issue Jul 13, 2023
@timothymillar
Initial implimentation of find-snvs tool PlantandFoodResearch#166
3f4988a
@timothymillar timothymillar mentioned this issue Oct 20, 2023
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timothymillar commented Oct 20, 2023 •
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Idea for arguments:

  • --maf: min population allele frequency (default = 0.0)
  • --mad: min population allele depth (default = 0)
  • --ind-maf: min individual allele frequency (default = 0.1)
  • --ind-mad: min individual allele depth (default = 3)
  • --ind-min: min number of individuals passing --ind-maf and --ind-mad (default = 1)

All filters are combined (intersection). This gives good flexibility and makes few assumptions about population size/structure for defaults.

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Fixed in #169

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