I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are failing.

 

1. With Unified genotyper it give me message saying Sequences are not currently available for specified build. I have hg19 related data and using default  settings  (pick up hg_g1k_v37 no other option). I am not sure why it is giving me this error.

2. As an alternative I tried to run Freebayes with default setting and choosing hg19 - it i snot giving any specific message but undetr bug icon gives me -killed.

 

Now in order to make sure my Bam is OK, I tested out side Galaxy mPile up and with in Galaxy pile up. Any suggestion why UNified genotyper is not working. If needed I can share my history.

 

Thanks.