I want to use the bwa mem algorithm to analysis my PE 100 seqdata (BWA Version: 0.7.12-r1039). I used "-M" option to mark the secondary alignment. Now i want to filter secondary alignment in sam file,my commands are:
bwa mem -t 20 -k 25 -M Ecoli.fa read1.fasta read2.fasta > read.sam
samtools view -H -S read.sam > split.sam
samtools view -F 256 -S read.sam | cat >> split.sam
But I want to shorten the analysis time,is there any options in bwa mem algorithm that can filter the secondary alignment directly?