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Problem in using TargetRealigner on bowtie mapped reads
I have Exome data from SOLiD 5500xl for which bowtie-0.12.8 was utilized for mapping. The SAM file obtained from bowtie does not have RG tag for every read and also the mapping Quality is 255 for the mapped reads both of which are unacceptable by GATK. By reading on GATK forum I tried appending the RG tag using picard AddorReplaceReadGroups utility which worked fine. Then I tried solving the mapping quality problem by using ReassignMappingQualityFilter but it does not work for me.
The command I used was:
java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -I bl_mark_duplicate.bam -R /share/reference/human/samtools/hg19.fa -rf ReassignMappingQuality -DMQ 60 -o bl_input.bam
But it does not reasign the mapping quality instead gives me the error of missing quality values.
I solved this problem by replacing the mapping quality value through perl script. After this again I tried using TargetRealigner, though it does not give me error but does not print any thing in output file.
If I just ignore this step and try to do baserecalibration then I get the following errror:
SAM?BAM file is malformed. unable to find color space information in Solid reads. Unfortunately this BAM file can not be recalibrated due to potential reference bias.
Please help me solve this problem. Hoping for a positive response.
Thanks and Regards,