I have recently encountered a problem, although I have seen the relevant solution here, but unfortunately I still can not successfully solve it，when I use gatk to call snp,I meet a error message:Lexicographically sorted human genome sequence detected in reads.after I looked for the solution,I tried the picard/resortsam.jar tool,but it did not work, so I see the read after do the resortsam to ensure the reads are in karyotypic order,follows are my some reads: INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchr8_gl000196_random38914 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchr8_gl000197_random37175 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchr9141213431 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchr9_gl000198_random90085 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchr9_gl000199_random169874 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchr9_gl000200_random187035 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchr9_gl000201_random36148 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchrM16571 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchrUn_gl000211166566 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchrUn_gl000212186858 INFO 2017-03-09 09:41:01 ReorderSam SN=%s LN=%d%nchrUn_gl000213164239 so I think if the problem is I have chrM or chrUn_gl00021116656 in my reads?
I would be grateful to hope that the enthusiastic people to help me,thanks
