[Samtools-help] Convert SAM to BAM help

[Marisa M. <mar...@ut...>]

Hello,
   I have a .bsp file (output file from BSMAP) that I have converted to 
a SAM file. When I try to use samtools to convert it into a BAM file I 
get the following error message:

[samopen] SAM header is present: 7 sequences.
[sam_read1] reference '1803809' is recognized as '*'.
Parse error at line 9: sequence and quality are inconsistent
Aborted

Shown below are the first lines of the input file:

@SQ     SN:1    LN:30427671
@SQ     SN:2    LN:19698289
@SQ     SN:3    LN:23459830
@SQ     SN:4    LN:18585056
@SQ     SN:5    LN:26975502
@SQ     SN:mitochondria LN:366924
@SQ     SN:chloroplast  LN:154478
@PG     ID:BSMAP_2.43
HWI-EAS157:7:1:748:1316#0/1             1803809 ++      255 65M     *
0       0 TTAGAGGTGGAGTGAATGGTAGTTTGTGAGGATGGAGGGGGTAGTGATTTAGATTGGAGAGTTG
A       UM NM:i:nC:1803809:1803810:1803821:1803825:1803828:1803832:1803835:
1803841:1803850:1803863:1803870 ZS:Z:0
HWI-EAS157:7:1:748:1814#0/1             10334968        -+ 255     65M
*       0       0 ATGAAGATTTGAAACGCGGTAGTGGAAAATGTTGGAGGAAGGGAATTGTAGATGAT
AAGAAATAG       UM NM:i:nC:10335031:10335025:10335024:10335003:10335000:103
34987:10334986:10334977:10334970        ZS:Z:1


Do you have any ideas about how I can convert this file to a BAM file?

   Thank you,
    Marisa Miller

-- 
PhD Candidate
Z.Jeffrey Chen Lab
The University of Texas at Austin
205 W. 24th St. Stop A4800
Austin, TX 78712
512-475-9335