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Old 10-23-2014, 11:10 AM   #1
Junior Member
Location: Asheville

Join Date: Nov 2010
Posts: 8
Default GATK Based Variant calling STEPS


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



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!
satishkumar is offline   Reply With Quote
Old 10-23-2014, 09:21 PM   #2
Location: Australia

Join Date: Mar 2011
Posts: 85

Dear Satish

I think if you follow the guidelines given here (as you are focusing on GATK):
then you cannot go wrong.
Good luck.
Elsie is offline   Reply With Quote

exome analysis, gatk, variant calling

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