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Thank you for your patience!
Hi, I am getting an error (no info given about causes unfortunately) following running BaseRecalibrator:
java -Xmx4g -jar $tool/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -I $bwa/BAM/s_1.rmdup_readgps.bam \ -R $bin/Bos_taurus.UMD3.1.66.fa \ -knownSites $bin/Bos_taurus_UMD_3.1.DBSNP.zero.ordered.bed \ -o $gatk/recal_rea/recal_data1.grp
I get output to screen of all chromosomes, positions etc followed by the error
chrX_dna:chromosome_chromosome:UMD3.1:X:1:148823899:1, chr1_dna:chromosome_chromosome:UMD3.1:1:1:158337067:1 #####ERROR------------------------------
Can you suggest any reasons for BaseRecalibrator giving up here? I understand the BED file is 0-based but it has been used successfully in the previous incarnation of BaseRecalibrator. I have tried the knownSites:mask,BED and it has no effect. I have all necessary readgroup info and index for BAM, and indexed BED.
Your help is much appreciated.