Hi,

I received 1.0 X WGS samples in fastq format. Each sample consist of two (sample1_1.fastq, sample1_2.fastq) fastq files.

Now I want to generate the .bam file and the question occurred.

My "bwa mem" command that works:

bwa mem ref.fastq -sample1_1.fastq, sample1_2.fastq | samtools sort -o output.bam

The question: Are there any parameters I should set in "bwa mem" tool that depend on the type of WGS data (1.0x vs 30x,...) in order to obtain optimal results?

Thanks.