Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Haplotype caller empyrean Bioinformatics 0 08-23-2012 06:44 PM
indel caller - GATK or Pindel, or anything else? caswater Bioinformatics 0 06-28-2012 10:11 AM
Haplotype calls from Amplicon Sequencing empyrean Bioinformatics 3 06-25-2012 02:27 PM
dubious SNP calls from GATK caswater Bioinformatics 0 04-24-2012 05:21 PM
GATK unified SNP caller error dakl Bioinformatics 4 11-23-2010 09:27 PM

Thread Tools
Old 11-29-2012, 06:51 AM   #1
Junior Member
Location: chicago

Join Date: Jan 2010
Posts: 5
Default GATK Haplotype caller missing calls

Hello friends,

I am using GATK Haplotype caller to call snps and indels from a GATK realigned, re-calibrated bam file (following GATK best practices). The only options I have changed from default values are -stand_call_conf and -stand_emit_conf, both set to 20. When I was comparing the GATK vcf file to samtools snp file for concordance I have noticed that GATK Haplotype caller missed some snps which look very real in IGV. Here is pileup for one of those snp positions from samtools (hg19)

8 6338306 C 140 ..A...A...A.a,...AAAA.,aA,.A...,,A,.A,a.aa,aaa.,.A,,A..,,AA.,.AAAAAa..,a,a,,,AAA.aA,aaa,,.AAaaaAAa,aa..,.a,a.Aa,.AA..,,aa,,,,A,aa,aaa,a,a,,a 000111111133;;55537:79;:<;<<;<<<<=<;=:<<::;;=<<<>:<<8<<<<<8<<<:=8<<;<<<==;<;==<<<=<;===<<<<=<<<==;;6:<<9<969<<77;<<<;321201./<-.0-/.0.0/./..

Also, samtools view shows that consensus base is "A"

8 6338306 . C A 168 . DP=140;VDB=0.0241;AF1=0.5;AC1=1;DP4=36,36,32,34;MQ=51;FQ=170;PV4=0.87,1,1,1 GT:PL:GQ 0/1:198,0,203:99

I have tried running GATK with both call conf and emit conf to 10 and still couldnt see this variant. I do not want to reduce these to 0 as it will result in lot of FP calls. Am I missing anything? Any help with this is very appreciated!

Thanks a lot!
Attached Images
File Type: png GATK.png (58.1 KB, 20 views)
nvteja is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:31 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO