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I'm running PrintReads with a dictionary file prepared by Picard, but without any index file. GATK prepares index file and then complains that
"Sequence dictionary and index contain different numbers of contigs".
When I run it without dictionary or index files, it creates them both, but then dies at chr2 - and this is no wonder, as the dictionary created via GATK has only every second contig (34 lines instead of 67).
I would appreciate your help, as at the moment I have no clue what is going on...
java -Xmx4g -jar picard-tools-1.77/CreateSequenceDictionary.jar R=~/genome/mm10/mm10.fa O=mm10.dict CREATE_INDEX=true
/this, for an unknown reason, creates only dictionary/
java -Xmx4g -jar ~/bin/GenomeAnalysisTK-2.1-11-g13c0244/GenomeAnalysisTK.jar -T PrintReads -I ../snp_calling/B0642/B0642.refSNPreal.bam -R ~/genome/mm10/mm10.fa -BQSR ../snp_calling/B0642/B0642.refSNPreal.recrgp -o ../snp_calling/B0642/B0642.recal.bam