GATK Based Variant calling STEPS

[satishkumar]

Hello,

I am working on putting together a workflow for calling variants using Haplotype called in GATK:

The process follow I currently follow is as below:

Mapping : BWA- MEM

Picard :SORT SAM: java -jar /opt/NGSTools/picard-tools-1.118/SortSam.jar INPUT=clean.bam OUTPUT=samsorted.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENTAdd/Replace GroupsReOrderSAM

++++++++++++++++++

GATK

1) RealignerTargetCreator
2) IndelRealigner
3) HaplotypeCaller :
java -jar /opt/NGSTools/GATK-3.2.2/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/data/GATK_test/gatk/ucsc.hg19.fasta -I realigned.bam -stand_call_conf 30 -stand_emit_conf 10 --min_base_quality_score 15 -o haplotype.raw.snps.indels.vcf

+++++++++++++++++++++++++++++++++++++++++++++++

Can any one help me to check if the above process flow looks good to determine variants (gene panel and exome based experiments)?

Suggestion would be highly appreciated!
Thanks,
Satish

[Elsie]

Dear Satish

I think if you follow the guidelines given here (as you are focusing on GATK):

https://www.broadinstitute.org/gatk/guide/best-practices?bpm=index

then you cannot go wrong.
Good luck.