From the GATK main page, one can create a user’s account to download the non-commercial use package.

MuTect VCF format posted here
MuTect2 documentation
Mutect2 has many good features and is designed to work for INDEL, but it does not produce signature context.

MuTect1 output format is NOT well defined

There was a good forum post on formatting question

Discerning the difference between two MuTect version output.

This is astonishingly goodpost

I am using Mutect and Mutect2 for WES project, and here are some useful document I collected overtime.

MuTect1 was part of the GATK component.

GATK protocol — revisit
It has been some time since I used GATK. Now, much improvement has been made and I would like to revisit this software for a WES project.

Here is one from SeqAnswer in 2012, but it is still very useful

samtools sort .bwa.bam .bwa.sort

#Index 
samtools index .bwa.sort.bam

#mark duplicate
java -Xmx5g -jar MarkDuplicates.jar INPUT=.bwa.sort.bam OUTPUT=.bwa.sort.deduped.bam METRICS_FILE=.duplicates REMOVE_DUPLICATES=TRUE VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=TRUE


#Realignment based on known insert sites (Using Java 1.7 from now on as required by GATK)
java -Xmx5g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R Reference.fa -I .bwa.sort.deduped.arg.bam -known 1000G_phase1.indels.hg19.vcf -known Mills_and_1000G_gold_standard.indels.hg19.vcf -o .realign.intervals -S LENIENT

java -Xmx5g -jar GenomeAnalysisTK.jar -T IndelRealigner -R Reference.fa -I .bwa.sort.deduped.arg.bam -targetIntervals .realign.intervals -known 1000G_phase1.indels.hg19.vcf -known Mills_and_1000G_gold_standard.indels.hg19.vcf -o .bwa.sort.deduped.arg.realigned.bam -S LENIENT

java -Xmx5g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R Reference.fa -l INFO -I .bwa.sort.deduped.arg.realigned.bam -knownSites 1000G_phase1.indels.hg19.vcf -knownSites Mills_and_1000G_gold_standard.indels.hg19.vcf -knownSites dbsnp_137.hg19.vcf -o .recalibration_report.grp -S LENIENT 

java -Xmx5g -jar GenomeAnalysisTK.jar -T PrintReads -R Reference.fa -l INFO -I .bwa.sort.deduped.arg.realigned.bam -BQSR .recalibration_report.grp -o .bwa.sort.deduped.arg.realigned.recalibrated.bam -S LENIENT