Entering edit mode
16 months ago
ZheFrench
▴
590
The @HD should be unique , no ? I don't get why it can be sorted and unsorted at the same time in a two lines header fashion.
samtools view -H sorted_test.bam |grep '@HD'
@HD VN:1.3 SO:coordinate
@HD VN:1.5 SO:unsorted GO:query
How did that happen? Were two headers joined together at some step manually? Strictly speaking that breaks the SAM format spec since only one
@HD
line is expected though it is optional.