Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

MuTect2 : Calling on triallelic_site by GATK v3.6 vs v3.7

HubertHubert South KoreaMember
edited April 2017 in Ask the GATK team

Here is different calling result on specific tri-allelic site using GATK v3.6 and v3.7.

[ Command ]
java -XX:ParallelGCThreads=6 -Xmx30g -jar GenomeAnalysisTK-3.6 (3.7) /GenomeAnalysisTK.jar
--disable_auto_index_creation_and_locking_when_reading_rods
-T MuTect2
-R hg19.fa
-I:tumor tumor.bam
--normal_panel normal_pane.vcf
--dbsnp dbsnp_138.hg19.vcf
--cosmic CosmicCodingMuts.sorted.vcf
--bamOutput v36 (v37)
-o v36.vcf (v37.vcf)
-L chr7:55,084,725-55,277,031

[ MuTect2 in GATK v3.6 ]
chr7 55266417 . T A . panel_of_normals;triallelic_site ECNT=1;HCNT=6;MAX_ED=.;MIN_ED=.;NLOD=0.00;TLOD=6.49 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:0,12:1.00:0:2:0.00:0,29:0:0

image

[ MuTect2 in GATK v3.7 ]
chr7 55266417 rs1140475 T C . panel_of_normals DB;ECNT=1;HCNT=55;MAX_ED=.;MIN_ED=.;TLOD=648.87 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:0,340:1.00:162:177:0.478:0,9585:0:0

image

[ Variant in PON, COSMIC, and dbSNP ]

image

I think 'A' allele is somatic mutation, but the result of GATK v3.7 is 'C' might germline mutation.
I've searched GATK forum, and found the post related to change method calling on triallelic site.
(http://gatkforums.broadinstitute.org/gatk/discussion/8386/mutect2-and-alternate-allele-calls)

I want to know what is difference of calling algorithm between GATK v3.6 and v3.7 on tri-allelic site.
Always thank GATK team :)

Issue · Github
by Sheila

Issue Number
1984
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answer

Answers

Sign In or Register to comment.