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

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

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
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Old 10-23-2014, 08:21 PM   #2
Elsie
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Location: Australia

Join Date: Mar 2011
Posts: 85
Default

Dear Satish

I think if you follow the guidelines given here (as you are focusing on GATK):
https://www.broadinstitute.org/gatk/...ices?bpm=index
then you cannot go wrong.
Good luck.
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exome analysis, gatk, variant calling

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