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IndelRealigner ERROR with canfam 3

mike_boursnellmike_boursnell Member
edited August 2012 in Ask the GATK team

When I run IndelRealigner I get an ERROR like this. It is a whole screen of chrUn something, ending like this:

chrUn_AAEX03026059, chrUn_AAEX03026060, chrUn_AAEX03026061, chrUn_AAEX03026062, chrUn_AAEX03026063, chrUn_AAEX03026064, chrUn_AAEX03026065, chrUn_AAEX03026066, chrUn_AAEX03026067, chrUn_AAEX03026068, chrUn_AAEX03026069, chrUn_AAEX03026070, chrUn_AAEX03026071, chrUn_AAEX03026072, chrM]

ERROR ------------------------------------------------------------------------------------------

The command is this:

java -Xmx8g -Djava.io.tmpdir=javatempdir -jar GenomeAnalysisTK.jar -T IndelRealigner -R canfam3.fasta -I ABC.realigned.rg.bam -targetIntervals ABC.bam.intervals -o ABC.clean.bam -known dummy_DBSNP.vcf -compress 0 -model USE_READS

Any ideas? It all works OK with canfam2 so it seems to be something to do with the canfam3 REF sequence.

Best Answer


  • Mark_DePristoMark_DePristo Broad InstituteMember admin
    Accepted Answer

    The error message tells you what's wrong. The ref and read references are incompatible.

  • Which error message is that sorry? I can't see one.

    When you say "the ref and read references are incompatible" what do you mean? The reference sequence is canfam3 and the fastq files are just sequence...

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    You need to view the entire error message (try piping it to a log file). Basically, your reads are probably aligned to canfam2 so you can't use a canfam3 reference. This is all described in our help documentation on this forum.

  • No it was all aligned to canfam3. But piping to a log file revelaed that it was the dbSNP file that was the source of the error. Thanks. For dogs I don't really want to filter out any SNPs as different breeds have different SNPs. How can I miss that out?

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