Hi,
I started recently using bwa mem. Using samtools flagstat on the alignment, I see that the total reads are less than the reads in the fastq file and the percentage of mapped reads is 100%.
How can I make bwa mem work the same way as bwa aln reporting all reads? Is it something with the -T parameter?
I started recently using bwa mem. Using samtools flagstat on the alignment, I see that the total reads are less than the reads in the fastq file and the percentage of mapped reads is 100%.
How can I make bwa mem work the same way as bwa aln reporting all reads? Is it something with the -T parameter?