BAM file not indexed
When I realigned reads around indels, an error occured:
The previous 2 steps and the realignment command lines are:
Could anyone tell me what's wrong with it? Thanks in advance!
When I realigned reads around indels, an error occured:
HTML Code:
ERROR MESSAGE: Invalid command line: Cannot process the provided BAM file(s) because they were not indexed.
Code:
java -Xmx4g -Djava.io.tmpdir=./ \ -jar picard-tools-1.57/SortSam.jar \ SORT_ORDER=coordinate \ INPUT=MK-5.sam \ OUTPUT=MK-5.bam \ VALIDATION_STRINGENCY=LENIENT \ CREATE_INDEX=true java -Xmx4g -Djava.io.tmpdir=./ \ -jar picard-tools-1.57/MarkDuplicates.jar \ INPUT=MK-5.bam \ OUTPUT=MK-5.marked.bam \ METRICS_FILE=metrics \ VALIDATION_STRINGENCY=LENIENT java -Xmx4g -jar GenomeAnalysisTK-1.6-9-g47df7bb/GenomeAnalysisTK.jar \ -T RealignerTargetCreator \ -R hg19.fa \ -o MK-5.bam.list \ -I MK-5.marked.bam java -Xmx4g -Djava.io.tmpdir=./ \ -jar GenomeAnalysisTK-1.6-9-g47df7bb/GenomeAnalysisTK.jar \ -I MK-5.marked.bam \ -R hg19.fa \ -T IndelRealigner \ -targetIntervals MK-5.bam.list \ -o MK-5.marked.realigned.bam
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