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.)
Thanks!
Max
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.)
Thanks!
Max