bwa mem algorithm filter secondary alignment

Question

[xudongyang]

Hello,everyone

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?

Thanks!

Answer 1

[Devon Ryan]

If you want to shorten the processing time, then use BAM everywhere.