DRAGEN-GATK short variant calling
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If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: latest version 4.2.2.0
No an error accures. However, I want to use the dragen-gatk model and Im using these command.
Is that correct?
Do I need to add any other parameter for dragen?
Is there a dragen aligner added in gatk?or only for variant calling?
/app/Genome/gatk-4.2.2.0/gatk ComposeSTRTableFile -R ../../genome/genome.fa -O Output_Germline_Aziz/hg19.str.zip
/app/Genome/gatk-4.2.2.0/gatk CalibrateDragstrModel -I Alignment_Germline_Aziz/$i.bam -O Output_Germline_Aziz/$i-DRgstr.txt -R ../../genome/genome.fa -str Output_Germline_Aziz/hg19.str.zip
/app/Genome/gatk-4.2.2.0/gatk HaplotypeCaller -R ../../genome/genome.fa -I Alignment_Germline_Aziz/$i.bam --dbsnp ../../recalset/dbsnp_132.hg19.vcf -O Output_Germline_Aziz/${i}_HaplotypeCall-dargen.vcf --dragstr-params-path Output_Germline_Aziz/$i-DRgstr.txt
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Hi Heba B abusamra,
I am going to move your post into our Community Discussions -> General Discussion topic, as the germline topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Pamela
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Hi Heba B abusamra,
Thanks for writing in about DRAGEN-GATK! We will releasing more documentation about how to use it within the next month.
We recommend that you use the Dragmap aligner when using the dragen parameters. It can be found here: https://github.com/Illumina/DRAGMAP
You'll first want to build a hash table from your reference then run the alignment step. In GATK, you'll run the commands you wrote above with one change: in HaplotypeCaller, make sure to specify --dragen-mode true. Hope this helps!
Best,
Genevieve
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