How to do with unproperly mapped pe reads?

[Applemelon]

Hi, I am a newbie in genome resequencing analysis. When I tried to use picard SortSam to sort pe reads, I found some reads are mapped in different chrosomes. How do you do with this case? Should I remove all such reads before sorting? What analysis can I do to these pe reads？ Thank you for your help.

FCC0A5LACXX:2:1101:1873:2244#ACAGTGAT 81 Gm16 6378912 37 90M Gm02 37092849 0 TACGCCTTTGAGCACGTATAGATCCTTTGATTATGTCTCGCCGAAAATCCGATTGTTGGGAATAACGTATTAAAGCCAATTCATTTTTTT @9@A?@>>BAC>DDCDCC>:<?DC@>C@CCC=A9>8GHEHIHCIJIGGGDHHGIGEEGAGGHFGHEIIJIJJJIIHHFDDDADDF@<@ RG:Z:CA109.1 XT:A:U NM:i:2 SM:i:37 AM:i:23 X0:i:1 X1:i:0 XM:i:2 XO:i:0XG:i:0 MD:Z:42A7A39
FCC0A5LACXX:2:1101:1873:2244#ACAGTGAT 161 Gm02 37092849 23 90M Gm16 6378912 0 ATATTTTTAGTTATTATCAATGAAGGTAATAGAATATATTTTCTAAGAATGGATTGGGTTATTAATAAAATACCTCTTATTACTTGAGCA @@@FFFFFFHDDHIJJJCHIHEIIHI@@CGGGIEHGGHGIIJGHIGGEGIFEEGIEHHGHGGHJDHIIGIHIIGG:FGGIGDHGEHHDFC RG:Z:CA109.1 XT:A:U NM:i:0 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:0 XO:i:0XG:i:0 MD:Z:90 XA:Z:Gm18,-37309287,90M,1;

[rboettcher]

I would not necessarily remove them. If there is more evidence (more read pairs) aligned in that way, you could look at chromosomal breaks/fusions which are quite common in cancer tissues.