I am running GATK's RealignerTargetCreator with this command:
java -Xmx36g -jar GenomeAnalysisTK.jar -S LENIENT -T RealignerTargetCreator -R human_g1k_v37.fasta -o SRR098359.interval_list -I SRR098359.bam -B:snps,VCF 00-All.vcf
The process quits with an error that includes this:
Cannot process the provided BAM file(s) because they were not indexed.
However, the bam file WAS indexed. I see the .bai file there. I recreated the index with the following command (in case something had gone wrong creating it):
samtools index SRR098359_sorted.bam
It created an identical .bai file and I ran RealignerTargetCreator again, and the same thing happened. Does anyone know what I'm doing wrong?
Thank you.
Eric
java -Xmx36g -jar GenomeAnalysisTK.jar -S LENIENT -T RealignerTargetCreator -R human_g1k_v37.fasta -o SRR098359.interval_list -I SRR098359.bam -B:snps,VCF 00-All.vcf
The process quits with an error that includes this:
Cannot process the provided BAM file(s) because they were not indexed.
However, the bam file WAS indexed. I see the .bai file there. I recreated the index with the following command (in case something had gone wrong creating it):
samtools index SRR098359_sorted.bam
It created an identical .bai file and I ran RealignerTargetCreator again, and the same thing happened. Does anyone know what I'm doing wrong?
Thank you.
Eric
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