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GATK4 Baserecalibration .GATKException: START (0) > (-1) STOP
I try t use GATK4 on my exome data. I try to do base-recalibration and I meet this error:
org.broadinstitute.hellbender.exceptions.GATKException: START (0) > (-1) STOP -- this should never happen, please check read: B0P8DQ1:88:CA2D7ACXX:1:2212:19066:92430 chr1:152084492-152084610 (CIGAR: 18D101M)
This is the command I use:
gatk-launch BaseRecalibrator -R /home/centos/illumina/database/hg19_primary.fa -I mapped_reads/merged_samples/433.dedup_rg.bam -knownSitesdatabase/dbsnp_138.hg19.vcf -O mapped_reads/merged_samples/433_recal.grp -VS SILENT
I use bioconda version of GTAK4 the last version