Command : java -jar gatk -T IndelRealigner -R refGenome.fa -targetIntervals sample1_sortedPos_rmdup_addRG_realn_targets.list -I sample1_sortedPos_rmdup_addRG.bam -o sample1_sortedPos_rmdup_addRG_realigned.bam
Output :
ERROR ------------------------------------------------------------------------------------------
ERROR AN INPUT FILE ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
ERROR This means that there is something wrong with the input file(s) you provided.
ERROR The error message below tells you what is the problem.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum until you have followed these instructions:
ERROR - Make sure that your BAM file is well-formed by running Picard's validator on it
ERROR (see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)
ERROR - Ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'
ERROR - Ensure that your CRAM index is not corrupted: delete the current one and regenerate it with
ERROR 'java -jar cramtools-3.0.jar index --bam-style-index --input-file --reference-fasta-file '
ERROR (see https://github.com/enasequence/cramtools/tree/v3.0 for details)
ERROR
ERROR MESSAGE: Exception when processing alignment for BAM index HWI-ST7001130:288:C2FLGACXX:4:2205:2442:86158 1/2 101b aligned read.
Files in directory :
sample1_sortedPosition_addRG_rmdup.bam (Bowtie2>BAM; Picard (BAM)> AddRG; Samtools(BAM)>removeDuplicates)
sample1_sortedPosition_addRG_rmdup.bam.bai
sample1_sortedPos_rmdup_addRG_realn_targets.list (GATK -T RealignerTargetCreator)
refGenome.1.bt2l
refGenome.2.bt2l
refGenome.3.bt2l
refGenome.4.bt2l
refGenome.dict
refGenome.fa
refGenome.fa.fai
refGenome.rev.1.bt2l
refGenome.rev.2.bt2l
refGenome.gff3