I'm using bam-readcount (version 0.7.4-unstable-35-0f3b356-dirty). Though it's version name doesn't exactly instill confidence, it is apparently the latest version available on github. Anyway, my problem is that it is failing to report on a large swath of my 17738 bp reference sequence. As shown below, bam-readcount output skips from position 8062 to 13923.
my_ref 8062 g 2 =:0:0.00:0.00:0.00:0:0:0.00:0.00 :0.00:0:0.00:0.00:0.00 A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 G:2:1.00:33.00:1.00:1:1: 0.04:0.01:35.00:1:0.01:75.00:0.50 T:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0: 0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 my_ref 13923 c 1 =:0:0.00:0.00:0.00:0:0:0.00:0.00 :0.00:0:0.00:0.00:0.00 A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 C:1:40.00:33.00:40.00:1:0:0.00:0.00:0.00:1:0.98:126.00:0.98 G:0:0.00:0.00:0. 00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 T:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0: 0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 enter code here
I have checked the bam file used as input to bam-readcount and have found that, while there are some gaps in covearage in this unrepresented interval, most of it is covered at about as well as regions that are represented in the bam-readcount output.
I've used three commands (shown below) but all give the same result.
bam-readcount -f my_ref.fa sample1-gsnap.bam.sort.bam my_ref bam-readcount -b 0 -q 0 -f my_ref.fa sample1-gsnap.bam.sort.bam my_ref bam-readcount -i -f my_ref.fa sample1-gsnap.bam.sort.bam my_ref
What am I doing wrong?
Thanks for your help