The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

Possible bug in BeagleOutputToVCF

LaurentLaurent Member, Broadie ✭✭
edited September 2012 in Ask the GATK team

Hi all,

It appears that BeagleOutputToVCF does not produce the expected result for the very first variant. Looking a little into it, I found out that the problem stems form the beagle.r2 file not having a header and the first line been treated as such instead of being read as a variant. Adding a bogus header line in the beagle.r2 file seems to be a fine workaround.



Sign In or Register to comment.