guidelines for BAM realignment in GATK 4

Dear all,
I have aligned my sequences with BWA and HISAT2, I would like to perform the realignment step. I find confusing reports over the internet on whether performing it or not. Can I ask if it is still a good practice to perform re-alignment and how can I run it?
I created a dictionary with
java -jar picard.jar CreateSequenceDictionary R=<ref.fa> o=<ref.dict>
But I do not have a vcf file. The syntax I have is:
java -jar GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R <ref.fa> \ # in the same folder there is the dict file
-I <file_dedup.bam>
-o <file.intervals>

(the -known option is skipped) followed by
java -Xmx8G -Djava,io,tmpdir=/tmp -jar /
GenomeAnalysisTK.jar \
-T IndelRealigner \
-R <ref.fa> \
-targetIntervals <file.intervals>
-I <file_dedup.bam> \
-o <file_indelrealigned.bam>

What would be the new syntax for GATK4?
Thank you,

Best Answer


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