Question: bwa mem algorithm filter secondary alignment
0
gravatar for xudongyang
2.0 years ago by
xudongyang0
xudongyang0 wrote:

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!

alignment • 1.0k views
ADD COMMENTlink modified 2.0 years ago by Devon Ryan84k • written 2.0 years ago by xudongyang0
2
gravatar for Devon Ryan
2.0 years ago by
Devon Ryan84k
Freiburg, Germany
Devon Ryan84k wrote:

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

ADD COMMENTlink written 2.0 years ago by Devon Ryan84k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1788 users visited in the last hour