Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

ReduceReads - No real operator (M|I|D|N) in CIGAR

mike_boursnellmike_boursnell Posts: 69Member

Hi. When I reduce my BAM files with ReduceReads and then run HaplotypeCaller I get this warning:

Ignoring SAM validation error: ERROR: Read name 1060, No real operator (M|I|D|N) in CIGAR

Why is this? Is it OK to inore it?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,235Administrator, GSA Member admin

    This sounds like the aligner was sleeping on the job... If it's just a few reads, I'd ignore it, or maybe use -rf BadCigar to filter them out so we don't risk choking on them later on. If it's more than a few, by all means check the alignments throughout the file.

    Geraldine Van der Auwera, PhD

  • taojinshengtaojinsheng Posts: 4Member

    Dear Geraldine, I encountered the same problem when running AddOrReplaceReadGroups tools from picard.Since the software exited when it met the first bad formatted read,I had no idea about the total number of such reads.Would you please explain more about the aligner was sleeping on the job? Thanks and regards.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,235Administrator, GSA Member admin

    Hi @taojinsheng,

    "sleeping on the job" is a colloquial phrase that means "doing something wrong". In this case it means that the aligner produced invalid output.

    One easy way of knowing how many reads are affected is to run the CountReads tool with the BadCigar filter enabled, like this:

    java -jar GATK.jar -T CountReads -R ref.fasta -I reads.bam -rf BadCigar
    

    When the run finishes, there will be a line in the console output that tells you how many reads were filtered out by BadCigar.

    If the percentage of bad reads is high, then you may need to do additional QC on your data and possibly realign them from the original FastQ.

    Geraldine Van der Auwera, PhD

  • taojinshengtaojinsheng Posts: 4Member

    I got it.Thanks a bunch,Geraldine.

Sign In or Register to comment.