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-rf BadCigar

newbie16newbie16 Member Posts: 42
edited August 2012 in Ask the GATK team

Hello,

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?

Thanks

Tagged:

Best Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,015 admin
    Answer ✓

    Hi there,

    You're not doing anything wrong, this is an issue that the tool is not handling properly. We'll fix it asap and post a notice in this thread when it's done.

    Geraldine Van der Auwera, PhD

  • ebanksebanks Broad InstituteMember, Administrator, Broadie, Moderator, Dev Posts: 698 admin
    Answer ✓

    Thanks for the feedback. I'll update the error message now.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

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