Ever wish you could automatically remove your unwanted output files from a submission without having to manually review them? If so, take this two minute survey and tell us more.
Latest Release: 1/10/19
Release Notes can be found here.

GATK "bwa_commandline" variable settings and comparisons to Bowtie2

Hi there,

I've been working on improving a workflow for processing data for my lab, and I wanted to compare the workflow we have set out to some of GATK's best practices workflows. We are currently using Bowtie2 and fgbio+picard to deal with our data.

My question is on the bwa mem command line written in the "processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json"

The bwa mem command line is: "bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta"
Looking at the manual page of bwa mem, I'm having a hard time finding out what these two variables are: -K and -Y. The two variables are not defined in the bwa mem manual page, so I don't really know what they are doing.

As for the 2nd part, I want to compare the results from alignment that we get from Bowtie2 and Bwa Mem using GATK's settings for BWA mem. Would you happen to know the closest parameters I can set for BT2, so that I can do an apt comparison when aligning? (We're using hg19.fa as the ref files.)


Best Answer


  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @Mchao

    I will pass this question to the firecloud team and @SChaluvadi Will be able to help you out with it.

  • MchaoMchao Member
    Thank you for the help!
Sign In or Register to comment.