ScoreDuplicates.pl Bug and Work-Around

[Mike Sovic]

Hi All,

It looks like ScoreDuplicates.pl in version 4.1 has a bug that causes the script to crash with an error message along the lines of…

Use of uninitialized value in split at ScoreDuplicates.pl line 212, <HAPLOTYPESB> line 56.
Use of uninitialized value $CurrentHaplotype2a in pattern match (m//) at ScoreDuplicates.pl line 217, <HAPLOTYPESB> line XX.
Use of uninitialized value $CurrentHaplotype2a in concatenation (.) or string at ScoreDuplicates.pl line 226, <HAPLOTYPESB> line XX.

We’ll get this fixed in the next version, but in the meantime, there are two options to get around it…

1.)  In your Replicates.txt file, which specifies the pairs of replicate samples, include ‘Individual’ at the beginning of the second name of each pair.  So, the file would look like…

Sample1            IndividualSample1b
Sample2            IndividualSample2b 

2.)  In the Haplotypes_X_Y.txt file that you’re using for the ScoreDuplicates.pl run (in the Output/Genotypes folder), remove ‘Individual’ from the beginning of all of the sample names.

Either of these approaches should work - don't need to do both.  Thanks L. Woodings for letting us know about this issue!