I use BWA-MEM to map reads to reference, the command line is below:
bwa mem -t 6 reference.fasta fq1.fastq fq2.fastq > result.sam
According to the source code, BWA will get read1 from the fq1.fastq, and get read1 from the fq2.fastq. By default, read1 and read2 are paired-end reads from the same DNA fragment. So, I think these two reads will mapped to the same chromosome, because any DNA fragment can't cross the chromosome. However, when I read the sam result of result.sam, there are many paired reads mapped to different chromosome! Why? According to my consideration, it is because of the structure variation or repeat sequence? Or any other reason? If I just want to call SNV and indel, may I remove these paired reads? Thanks in advance!