Code:
samtools view -S -f 0x100 <file.sam>
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Runto get the multimappers. -
BWA MEM question
Dear all,
I just have a question about bwa mem alignment. I ran the following simple command:
bwa mem <fa> <fastq> -t 5
Before the alignment I checked the number of reads with fastqc and then after alignment I counted the IDs present in the sam file with grep '<common ID> | wc -l and I got different results.
What causes the difference? Is the multi-mapper reads present in the sam file?
Total reads: 24 961 320
Aligned reads: 24 961 535
Thank you for the answere,
Regards,
Liy
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