Can BWA MEM input file be in fasta format?

Question

[biolab]

Hi, everyone,

I have a simple question: does bwa mem accept fasta format input file? The bwa mem help does not cover this issue, and no options for fasta input (bowtie has -f option), so I ask you here. Actually I made a test, and it seems ok, but I am not completely sure. THANKS a lot!

[mxs]

I am a bit out-of-date when it comes to BWA but if I recall correctly: you can use fasta format for ref. genome and reads but then you are neglecting the quality score information, that is, you are assigning some artificial quality score value.

Please, someone correct me if I am wrong. I am also curious.

mxs

Answer 1

[GouthamAtla]

It can handle fasta files. But it will NOT print dummy quality values in the SAM/BAM file. It prints * in the quality field. You should be careful with downstream analysis. If any tool expects a quality value, it may fail.

[biolab]

Thank you Geek_y and mxs. Yes, the quality score is missing. I will be careful in downstream analysis.