admixTools convertf error on ped file: "snp order check fail; snp list not ordered"
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3.9 years ago

I am trying to run the convertf tool in AdmixTools, as I have successfully run before. I am getting an error (warning perhaps? Because it appears to run to completion..?) that "snp order check fail; snp list not order". I built the original vcf file using GatherVCFs in GATK4 (previously CatVariants, GATK3), gathering the snp-called (HaplotypeCaller command) files in the order they were generated in, then used vcftoolsto output ped/map format files.

My command:

convertf -p par.PED2EIGENSTRAT

Printed to screen:

parameter file: par.PED2EIGENSTRAT

**warning: dubious parameter, please check the parameter name

## convertf version: 5000
genetic distance set from physical distance
snp order check fail; snp list not ordered: (processing continues)   23  1381 138077
zzz 509783 543784
snp order check fail; snp list not ordered: (processing continues)   23  1381 138136
zzz 509784 543785

genotype file processed

numvalidind:     35  maxmiss: 35001

eigenstrat output

##end of convertf run

I have not yet found a similar error online, and although convertf seems to finish, it does not produce a .geno file.
Any ideas on how to fix this issue would be greatly appreciated!

convertf ped snp admixtools • 2.1k views
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heys, I'm having a similar error, did you solve it?


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