I'm aligning mouse exomeseq (tumor and control) with bwa and hisat2. After comparison of the 2 alignments I see in many genomic positions strange reads with many mismatch aligned by BWA that are descarded by hisat2. Please could you give a feedback about the reasons for which BWA maps these reads? I suppose that them don't contain true variants but technical artifacts. The same reads are descarded by hisat2.
Here are the parameters for bwa mem and hisat 2
bwa mem: bwa mem -M -t 30 selection of reads samtools view -@ 30 -f 0x0002 -h -q 1 -F 4 -F 256
hisat2: --no-spliced-alignment --phred33 (remaining parameters default) selection of reads with NH:1/
I attach an example
thank you very much