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I used gatk HaplotypeCaller with parameter --do-not-run-physical-phasing false, some missing genotypes were phased to ".|.". What I was expecting was this "./. ", and it will turn to haploid "." after vcftools(0.1.17) recode processing.
So, I have to use gatk HaplotypeCaller --do-not-run-physical-phasing true to avoid phasing processing.
The text was updated successfully, but these errors were encountered:
Bug Report
Affected tool(s) or class(es)
gatk HaplotypeCaller --do-not-run-physical-phasing false
Affected version(s)
gatk-4.4.0.0
Description
I used gatk HaplotypeCaller with parameter --do-not-run-physical-phasing false, some missing genotypes were phased to ".|.". What I was expecting was this "./. ", and it will turn to haploid "." after vcftools(0.1.17) recode processing.
So, I have to use gatk HaplotypeCaller --do-not-run-physical-phasing true to avoid phasing processing.
The text was updated successfully, but these errors were encountered: