Service Notice: Due to the blizzard currently hammering the US Northeast, the Broad is shut down and the GATK forum will be mostly unattended while we hunker down and sip hot cocoa with marshmallows. Assuming the power stays on and we're able to dig ourselves out of the snow when it's all over, normal service should resume Wednesday or Thursday.

ReduceReads and scatter/gather

evakoeevakoe Posts: 25Member
edited September 2012 in Ask the GATK team

Hallo everyone, I have a question about ReduceReads when using scatter/gather. In the argument details of ReduceReads you write for the parameter -nocmp_names: "... If you scatter/gather there is no guarantee that read name uniqueness will be maintained -- in this case we recommend not compressing."

Do you mean, that if I use scatter/gather, I should use ReduceReads with the -nocmp_names option so that the read names will not be compressed OR do you mean that I should not use ReduceReads at all when scatter/gathering.

I assume the first is meant, I just wanted to make sure. Thank you for your time and effort. Eva

Post edited by Geraldine_VdAuwera on

Best Answer

Answers

Sign In or Register to comment.