BWA- SAM tools alignment default parameters

Question

[bestone]

hello, I will do whole genome sequencing in apricot. I should do an alignment with my data. I think that I need default parameters to do an alignment. How can I find the default parameters? Can you help with this issue?

[GenoMax]

If you do not change a parameter value then the program uses the defaults built in automatically. So simply run bwa with the minimum information needed. This should be fine in most instances.

bwa index ref.fa
bwa mem ref.fa reads.fq > aln-se.sam
bwa mem ref.fa read1.fq read2.fq > aln-pe.sam

Normally you do not need to make sam files as shown above. You can directly pipe the output into samtools to create the final sorted BAM file. With that said, if you are starting to learn then you could go step by step. Create SAM files and then convert to BAM using samtools.

[bestone]

Thank you for all your help.

Answer 1

[ATpoint]

Default parametery are those that are set when running a tool without modifications. Please read the manuals, both bwa and samtools are well-documented.