Proper Bowtie2 settings for snp calling applications

Question

[Denis]

Hi,

I'd like to map illumina paired-end reads to the reference genome by Bowtie2 for downstream snp calling with Freebayes. The reads are already adapters and quality trimmed. I plan to specify the following Bowtie2 options:

--end-to-end
--very-sensitive
--no-mixed
--no-discordant

I'm wondering which options i have to include/change in my Bowtie2 command line to produce the most reliable results.

Regards,
Denis

Answer 1

[ATpoint]

My recommendation is to use bwa mem with default settings which has proven a gold standard over the years. Bwa is expected and tested by almost any variant calling pipeline. No need to use anything else.