[Samtools-help] CleanSam not cleaning weird CIGAR introduced by GATK indel realignment

[Richard P. <rpe...@we...>]

Hi

I have the following two lines in my bam file, which was created by 
GATK's IndelRealigner

HS24_10061:8:1211:14598:53164#80        73      AAKM01002280 649 47      
91M2D9M0S       =       649     0
HS24_10061:8:1211:14598:53164#80        133     AAKM01002280 649 0       
*       =       649     0

When I run ValidateSamFile on this I get the following two errors, as 
expected:

# ERROR: Record 33489375, Read name HS24_10061:8:1211:14598:53164#80, 
CIGAR element with zero length
# ERROR: Record 33489375, Read name HS24_10061:8:1211:14598:53164#80, 
CIGAR M operator maps off end of reference

However, CleanSam doesn't seem to be able to fix these reads. Is there 
any tool I can run to clean up these reads with strange CIGAR strings 
with 0S at the end? Any chance of a change to CleanSam to help it catch 
cases such as this?

Thanks

Richard