dupcheck testpairs option

[Mark]

Hi 

I am trying to use dupcheck with the --testpairs=FILE option. 

I have set up a data file with two samples I know are duplicates, and dupcheck runs fine. When I add the option above, the command still runs, but no longer finds the duplicates. 

I was wondering what format and layout the file containing the pairs needs to have. 

So far I have tried a .txt file with two columns, tab separated, comma separated, with and without headers. 

Thanks

Mark

[Kevin Jacobs <jacobs@bioinformed.com>]

Hi Mark,

  

The pair file should be tab delimited with two sample names per line with no headers.  Please let me know if you're still having problems.

-Kevin

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[Mark]

Hi 

I did some more tests, and it seems that to use the --testpairs option, the SNP data file must be in sbat or sdat format 

(the user manual says that sbat/sdat is the preferred input for qc.dupcheck, but not the exclusive input).  

So, for example,

glu qc.dupcheck input.X -o dupcheck_out.txt

works fine regardless of the input format (X=sbat/sdat/lbat/ldat), but

glu qc.dupcheck input.X --testpairs.txt -o dupcheck_out.txt 

only works for sdat/sbat formats. 

Sorry if that's already in the help pages somewhere. 

Mark