Open GoogleCodeExporter opened 9 years ago
Hi,
All three of your SAM header lines have extra tabs at the end. This is against
the SAM specification and as such, it causes BAMTOOLS (the BAM liubrary that
bedtools uses to be unable to properly read the header. If I remove the extra
tabs and convert the result to BAM, all is well.
The "^I" symbols below are TABs.
cat -t test.sam
@HD^IVN:1.4^IGO:none^ISO:coordinate^I^I
@SQ^ISN:chr9^ILN:124076172^I^I^I
@RG^IID:sample1^IPL:IONTORRENT^ILB:lib1^ISM:sample1^I
DI8BD:05389:09916^I0^Ichr9^I57332309^I3^I54M712N47M^I*^I0^I0^ICACAAACACTTTACATGG
ACCTTCATGTCAAACTTGGTTTACCCAGGATCATTCCACAGGGATAACTGGCTTGTGGCGGCCAAGCGTTCATAGCGACG
TCG^I5558849;::@28////*0:5=7;<=999;;58:7<077*788*5:477///)/)0088:2::;688848<4889
388486:6:999268::8:8/////,^IX2:i:40^IMD:Z:101^IRG:Z:sample1^INH:i:4^IHI:i:1^INM:
i:0^ISM:i:3^IXQ:i:40^IXS:A:-^IXV:i:0^IXW:i:0
Original comment by aaronqui...@gmail.com
on 24 Sep 2013 at 4:37
perfect! It works for me too. Our BAMS came from GSNAP so we are
alerting the author of that tool as well.
Thank you so much.
Original comment by sonia.le...@gmail.com
on 24 Sep 2013 at 4:50
scratch that - seems we post-processed GSNAP and introduced the error
ther, so the GSNAP output is fine.
Original comment by sonia.le...@gmail.com
on 24 Sep 2013 at 4:52
Original issue reported on code.google.com by
sonia.le...@gmail.com
on 24 Sep 2013 at 3:02