Question: bwa mem algorithm filter secondary alignment
gravatar for xudongyang
22 months ago by
xudongyang0 wrote:


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?


alignment • 932 views
ADD COMMENTlink modified 22 months ago by Devon Ryan81k • written 22 months ago by xudongyang0
gravatar for Devon Ryan
22 months ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

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

ADD COMMENTlink written 22 months ago by Devon Ryan81k
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