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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Restarting a stopped UG run, pick up where it left off, does multithreading interfere?

TristanTristan La Jolla, CAMember
edited May 2013 in Ask the GATK team

Sometimes, while running the UnifiedGenotyper with -nct 8, my job might die for any number of reasons unrelated to your fine software. Can I start my next attempt, where the last one left off, simply by using the -L flag to specify the last genotyped location from the vcf output (and the rest of the genome)?
This of course works, but the deeper question is this - since I used the -nct flag, might some of the threads have been scanning ahead in the genome and therefore the last genotyped location in that vcf is too far ahead and I might miss some intermediate variants? My sincere apologies if this has already been asked, I did look around first.

Post edited by Tristan on

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