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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Failure to load kinship file made with vcf2kinship #78

Open LindaETV opened 5 years ago

LindaETV commented 5 years ago

Hi!

I recently started working with rvtest and am getting an error message related to the kinship matrix when attempting to run GWA. I have created a kinship matrix (called matrix.kinship) using the provided function vcf2kinship from program version 20190205. However, for a sample with fid 12345 and iid 12345, the kinship matrix shows fid 12345_12345 and iid 12345_12345 When I attempt to run my GWA, the imputed genotype file and phenotype file seems to link properly, as participants with missing phenotypes are correctly excluded. However, I keep getting the error message below:

[ERROR] Cannot find sample [ 12345 ] from the kinship file! [ERROR] Failed to load kinship file [ file.path/matrix.kinship ] [ERROR] Failed to load autosomal kinship (you may use vcf2kinship to generate one).

The sample fid and iid are the same between the imputed genotype vcf file, phenotype file and the input file that I used to make the kinship file. The referenced sample 12345 is the first sample in all files. Can the cause for this error be the fact that vcf2kinship has changed fid and iids? If so, how can I prevent this? If not, what could be the cause for this problem?

Many thanks in advance for any help you could provide!

Best, Linda

zhanxw commented 4 years ago

Sorry for the inconvenience. Let me investigate this a bit more.