How to use bwa mem for paired-end Illumina reads
we would like to use the bwa mem algorithm for the alignment of paired-end (100 bp) Illumina reads and variant calling
with GATK. Unfortunately there are some problems understanding the command description.
Do I need to use the -p and [mates.fq] options for paired-end reads?
And what about simply using the command below?
bwa mem -M -t 16 ref.fa read1.fq read2.fq > aln.sam
Command description (http://bio-bwa.sourceforge.net/bwa.shtml):
"If mates.fq file is absent and option -p is not set, this command regards input reads are single-end. If mates.fq is present, this command assumes the i-th read in reads.fq and the i-th read in mates.fq constitute a read pair. If -p is used, the command assumes the 2i-th and the (2i+1)-th read in reads.fq constitute a read pair (such input file is said to be interleaved). In this case, mates.fq is ignored. In the paired-end mode, the mem command will infer the read orientation and the insert size distribution from a batch of reads.
The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for long sequences. However, some tools such as Picard’s markDuplicates does not work with split alignments. One may consider to use option -M to flag shorter split hits as secondary."
We appreciate your help!