Whe 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.
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.
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