Dear sir,
When I use
[debbie@server GATKtest]$ java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R mysample.bam -D ~/dbsnp_138.b37.vcf -o myfile.HapCall.snp.g.vcf
it comes Error below:
INFO 01:06:58,830 HelpFormatter - ----------------------------------------------------------------------------------
INFO 01:06:58,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 01:06:58,832 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 01:06:58,833 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 01:06:58,833 HelpFormatter - [Sun Jun 18 01:06:58 CST 2017] Executing on Linux 3.10.0-514.10.2.el7.x86_64 amd64
INFO 01:06:58,833 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_121-b15
INFO 01:06:58,836 HelpFormatter - Program Args: -T HaplotypeCaller -R 5.C56_mark.bam -D /home/debbie/project/bundle_b37/dbsnp_138.b37.vcf -o 6.C56.gatk.HapCall.snp.g.vcf
INFO 01:06:58,840 HelpFormatter - Executing as debbie@tiger on Linux 3.10.0-514.10.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_121-b15.
INFO 01:06:58,840 HelpFormatter - Date/Time: 2017/06/18 01:06:58
INFO 01:06:58,840 HelpFormatter - ----------------------------------------------------------------------------------
INFO 01:06:58,840 HelpFormatter - ----------------------------------------------------------------------------------
INFO 01:06:58,855 GenomeAnalysisEngine - Strictness is SILENT
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: Fasta index file mysample.bam.fai for reference mysample.bam does not exist. Please see https://software.broadinstitute.org/gatk/documentation/article?id=1601 for help creating it.
ERROR -----------------------------------------------------------------------------------------
How do I generate a .bam.fai file?