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Additional info fields #174

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5 of 6 tasks
timothymillar opened this issue Mar 2, 2024 · 1 comment
Closed
5 of 6 tasks

Additional info fields #174

timothymillar opened this issue Mar 2, 2024 · 1 comment
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enhancement New feature or request vcf format

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@timothymillar
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timothymillar commented Mar 2, 2024 •
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Some additional (optional) info fields that would speed up filtering etc.

  • MCIP/MCIT MCI: proportion/count of samples found with evidence of Markov chain incongruence
  • SAFP ACP: sum of posterior allele frequencies (less issue with rounding in larger populations)
  • SAOP AOPSUM: sum of posterior allele occurrence (interpreted as number of samples in which an allele occurs)
  • CIGAR (length A): alternative to SNVPOS see Add CIGAR string for variants. #105
  • NLOC: number of variable loci (count of values in SNVPOS)
  • UAN: Count of unique in state alleles
@timothymillar timothymillar added enhancement New feature or request vcf format labels Mar 2, 2024
timothymillar added a commit to timothymillar/MCHap that referenced this issue May 10, 2024
@timothymillar
Add more optional --report fields PlantandFoodResearch#174
f3fabf9 
- Allow specification of INFO and FORMAT field variants
- Add ACP field
- Add INFO/AOPSUM field
- Add SNVDP field
@timothymillar timothymillar mentioned this issue Sep 10, 2024
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Done in v0.10.0

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