To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

-rf BadCigar

newbie16newbie16 Member
edited August 2012 in Ask the GATK team


I have a bam file where few reads have CIGAR strings that start with Deletions. For example: 440H1D33M1I1D33M.
I am trying to execute BaseRecalibrator (2.0 beta) on this file. However, I see an error below:

"##### ERROR MESSAGE: SAM/BAM file SAMFileReader{/home/datarig/CGP/GatkAnalysis/NG_2012_05_10_v2.6/WithGATK2.0/with_SamV2/NG_R1/test.ordered.sorted.realigned.bam} is malformed: Read starting with de
letion. Cigar: 440H1D33M1I1D33M. This is an indication of a malformed file, but the SAM spec allows reads starting in deletion. If you are sure you want to use this read, re-run your analysis with
the extra option: -rf BadCigar"

However if I use the -rf BadCigar filter, I still get the same error. The command I used is pasted below.

"java -Xmx4g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -I test.bam -R ucsc.hg19.fasta -knownSites dbsnp_135.hg19.vcf -o recal_data.grp -rf BadCigar"

Could you please let me know what I am doing wrong?



Best Answers


Sign In or Register to comment.