gatk bam is malformed

[carolW]

Hi,
I got the following error message after invoking gatk

ERROR MESSAGE: SAM/BAM file /home/carolw/NGS/data/SRR062641.filt.marked.bam is malformed: SAM file doesn't have any read groups defined in the header.

but I just got the MAPQ should be 0 for unmapped error when I ran bwa to generate sam and bam files. according to the forums, this error should be ignored. So whether the gatk problem comes from the bwa problem or warning or not, how to solve the problem?

Please see the attached file for the outputs of bwa and gatk

Look forward to your reply,

Carol

[swbarnes2]

It says there are no read groups. Did you run bwa so that it would add read groups? Did you run a program to add read groups in after the fact?

If the answer to those questions is "no" or "I don't know" then your problem is likely there.

[carolW]

I added read groups when calling bwa.

Now I get 2 different error messages when I run gatk

If I use the output of picard markedduplicate, I get error message on unindexed bam file whereas the bam file is already indexed as it is already generated by picard samsort before invoking picard markedduplicate. bai file exist too.

And if I use the output of picard sortsam directly, I get
ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'

-----------------------------------
java -jar SortSam.jar SO=coordinate INPUT=~/NGS/data/SRR062641.filt.sam OUTPUT=~/NGS/data/SRR062641.filt.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true

~/NGS/pgm/GenomeAnalysisTK-2.4-9-g532efad$ java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R /home/carolw/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -o ~/NGS/data/SRR062641.filt.bam.list -I ~/NGS/data/SRR062641.filt.bam

ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'

-----------------------------------------------------------
java -jar MarkDuplicates.jar INPUT=~/NGS/data/SRR062641.filt.bam OUTPUT=~/NGS/data/SRR062641.filt.marked.bam METRICS_FILE=metrics VALIDATION_STRINGENCY=LENIENT

java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R /home/carolw/NGS/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -o ~/NGS/data/SRR062641.filt.bam.list -I ~/NGS/data/SRR062641.filt.marked.bam

ERROR MESSAGE: Invalid command line: Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.