Entering edit mode
6.4 years ago
Darren Lin
•
0
The BAM file I am dealing with consist some alignments with extremely large insert size.
For example:
H06HDADXX130110:1:1214:13197:7463 145 20 1361711 60 41S147M62S = 61590101 60228245
H06HDADXX130110:1:1214:13197:7463 97 20 61590101 60 242M8S = 1361711 -60228245
What's going on with this kind of alignment?
Thanks!
This should be changed to a question.
It could be; bad alignment, specially if it is a repetitive genome and this sequence exists in different location on the genome, or may be any kind of structure variations.
try to add to your question the BWA command that you used for alignment.
hm....thanks, but I can not just filter "properly paired" flag. I can probably set a threshold to limit the maximum deletion.
yes you can with
samtools view -F 2