bad input error on the PrintRead step
To detect the mutation on the bam file, I used GATK to calibrate the file currently. However, only one showed this kind of error when I used PrintRead mode. The version of program is 3.5
Input: java -Djava.io.tmpdir=./scratch -Xmx4g -jar -GenomeAnalysisTK.jar \
-R ucsc.hg19.fasta \
-T PrintReads \
-I C2_fixed.bam \
-BQSR C2_recal_data.grp \
Error occurred in this step was as below.
Bad input: The GATK report has an unknown/unsupported version in the header: chrM:66-526
Could you give me some comments about this problem? This is first time I got this kind of error.
Thanks in advance.