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commands to for variant calling

Hello, I need help running the gatk program for my .fastq files. every time a get a step ahead I run into errors that take me days/weeks to resolve. I know there's a better way, I just can not find it. Would you please give me a sequential list of commands, going from .fastq to the VCF file? I have been working on these files since December 2018 and still struggling at the MergeBamAlignment step.
the current error I have is
Error parsing SAM header. Unrecognized header record type.
Your help is very much appreciated.


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