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ERROR : BAM file has a read with mismatching number of bases and base qualities

abaanoabaano Member
edited August 2012 in Ask the GATK team

Dear GATK team,

I am trying to understand/resolve this issue with my bam files. I have been been using GATK tools for a while. However, recently I started seeing this error. I understand there are two possible means to silence there errors one being the MalformedReadsFilter, which I learned is on by default. Also there is the -defaultbasequalities=-1 in GATK. So my question is why am I still seeing this error, and why does it blow up GATK. From what I understand both methods deal with the same type of issue. It is very likely that I am missing something so please fell free to enlighten me :) Thank you

It happens with indelrealigner. I have not tested other GATK tools. With GATK v1.5 the same bam file works fine however with v2.1.5 it errors our. the error I get is ##### ERROR MESSAGE: SAM/BAM file SAMFileReader{something.bam} is malformed: BAM file has a read with mismatching number of bases and base qualities. Offender: SOLEXA:1:40:1371:7#1 [1 bases] [0 quals]

Any suggestions are greatly appreciated.

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