# BWA doesn't recognize HiC options

I'm trying to run bwa on HiC data. This is the command I'm giving:

bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq


and here's the error message:

mem: illegal option -- 5


Supposedly, the 5SP option is for HiC data (cite), but my BWA isn't recognizing it. Anybody have any ideas? My initial thought is to update BWA to the newest version, but I don't want to mess with our replicatibility since I am new to the lab and don't want to be updating software when I don't need to. The server is a Mac Pro and bwa version is 0.7.12-r1039. Thanks.

• You can use conda to install and test the desired version of bwa to test. This will not interfere with whatever version installed on the server.
– haci
Oct 12 '20 at 9:29