Figure out how to run bwa-mem

[billingross]

bwa command line from GATK: bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta

bwa mem reference page: https://bio-bwa.sourceforge.net/bwa.shtml

What the options mean:

-K: minimum seed length (ignore this)
-p: assume the input file is interleaved paired-end Fast (ignore this)
-v: verbosity level, 3=normal (fine)
-t: number of threads (don't need 16)
-Y: I don't know what this does

[billingross]

How to write reads directly to BAM:

bwa mem genome.fa reads.fastq | samtools sort -o output.bam

[billingross]

Command I'm going to use:

bwa mem -t 2 -v 3 ~{reference_fastq} ~{reads_1} ~{reads_2} | samtools sort -o {output_bam}