The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.