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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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suppy vcf2kinship with known pedigree information (--ped has no effect) #79

Closed scogi closed 4 years ago

scogi commented 5 years ago

Hi!

I just started using rvtests to analyze related samples (families) andn was wondering what the correct way is to supply vcf2kinship with known family structure. The help page tells to use --pedigree to supply vcf2kinship with known pedigree structure (https://github.com/zhanxw/rvtests#related-individual-tests), but this gives the error "unparsed arguments: ---pedigree pedigree.ped. I then tried --ped (info from the help page within the terminal). Vcf2kinship runs trough, but the log file tells "[WARN] Warning: Specified parameter --ped has no effect." Indeed there is no difference in the generated matrix whether only --bn is used or also --ped is specified. Am I missing something? The ped file is the same holding the phenotype data. Is this an issue?

Thank you!

best regards Stefan

zhanxw commented 4 years ago

You're right that the ped file was not used. That is the expected behavior, as --bn will use the observed genotypes to calculate the kinship. That's the recommended behavior when you have many samples.

scogi commented 4 years ago

Thank you. I found my error(s). I had specified --bn, too, although i just wanted to supply a known pedigree file using --ped. Additionally I had additionally specified as second input, additionally to the ped file.

As a side note: the documentation is ambiguous about the --ped option. At http://zhanxw.github.io/rvtests/#related-individual-tests and https://genome.sph.umich.edu/wiki/Rvtests#Related_individual_tests the documentation says

You can specify --ibs to obtain IBS kinship or use --pedigree input.ped to calculate kinship from known pedigree information.

I think it should read as follows, right?

You can specify --ibs to obtain IBS kinship or use --ped input.ped to calculate kinship from known pedigree information.

Using --pedigree gives the error "unparsed argument" to me.

cuihaoyue commented 3 years ago

HI, do you use the known pedigree information successfully? I met the same error: [WARN] Warning: Specified parameter --ped has no effect. And then I rm the --bn, like : vcf2kinship --inVcf input_5.vcf.gz --ped phenotype.ped --out xxxxx I got the error: [INFO] Empiricial kinship will be calculated. [WARN] Warning: Specified parameter --ped has no effect. [INFO] Start creating empirical kinship from VCF file. [INFO] Using default maximum missing rate = 0.05 [INFO] Using default minimum MAF = 0.05 [ERROR] More than one or none of the empirical kinsip calculation methods specified.