BWA alignment using paired end reads from different lanes

[deepue]

Hi,

I would need some help on to proceed for WES analysis.

I observed from different posts in the forum that the paired end reads can be aligned separately and the resulting SAM files are merged for further analysis. I would like to know on how to consider the data from different lanes while doing alignment.

Should i merge the data from different lanes for L{1,2}_R1.fq, L{1,2}_R2.fq into separate files or perform alignment for different read type(1,2) and different lanes specific data separately(4 times L1_R1.fq, L1_R2, L2_R1, L2_R2) and merge the SAM files for further analysis ?

Please advise.

Thanks

[lindenb]

cross posted: https://www.biostars.org/p/136497/