AGeNT LocatIt

Question

[jhy]

Hi, I'm using AGeNT LocatIt to mark duplicates of WES data.

command line: java -Xmx32G -jar LocatIt_v4.0.1.jar -U -X deduptemp -IB -OB -C -i -l SureSelect_v6_geneAnno.bed -o outBam inBam UMIfastq

There is no error message, but the work continues to not finish. Can I know the reason why one sample doesn't finish after a few days even though other samples finished in a few hours?

Thanks

Answer 1

[Greg]

Give it more memory.

~10x more memory, or whatever you can give it,

I had samples that weren't even close to being done after 3.5 days, where upping the memory led to them being processed in 9 hours. LocatIt needs a lot of memory, and will slow down a lot if it doesn't get it

[barslmn]

He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?