running bwa in pair end reads

Question

[luzglongoria]

Hi friends,

I would like to run bwa in my reads (12 pair end reads = 24 samples) and create a .sam file as an out put.

I want to use the command:

bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam

My question is if I can use an unique command for all my 12 pair reads or I have to run 12 different commands (one per pair end read).

Any help is more than welcome :)

Answer 1

[Devon Ryan]

You need a separate command per pair of reads.

[luzglongoria]

Thanks !

The thing here is that I want a final .bam file for working with freebayes. Reading the freebayes manual it seems like I need a unique .bam file. Shall I merge the .sam files resulting from bwa, create a .bam file and then work with it on freebayes?

Does it make sense?

[Pierre Lindenbaum]

Shall I merge the .sam files resulting from bwa, create a .bam file and then work with it on freebayes?

yes