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Variant calling: Bam file is indexed but GATK thinks it is not

Trying to call variants from a bam file with the command below:

java -jar /usr/local/softw/GenomeAnalysisTK.jar -T UnifiedGenotyper -I LBK_Lipatov2014_DS2X.bam -R /mnt/NAS/share/Ref/human/hs37d5.fa -L 1000G.bed --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -o LBK_Lipatov2014_DS2X_GATK.raw.vcf

I get the error below that says the bam is not indexed. But I did index the file and it is present in the same folder as the bam. (I did the sorting and indexing with samtools if that makes a difference.)

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
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 unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: Cannot process the provided BAM/CRAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAM/CRAMs in --unsafe mode, but this feature is unsupported -- use it at your own risk!

What can I do?

Answers

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