SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cufflinks reports extremely high FPKMs for short transcripts cram Bioinformatics 10 11-24-2014 04:24 PM
how to calculate the genome heterozygosity luckylove De novo discovery 0 06-19-2012 05:16 PM
GATK UnifiedGenotyper heterozygosity parameter manducasexta Bioinformatics 0 04-17-2012 12:08 PM
Extremely high cy3 signals chenglei SOLiD 3 10-05-2011 07:14 AM
GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment nullalleles Genomic Resequencing 1 07-18-2011 06:28 AM

Reply
 
Thread Tools
Old 12-11-2012, 12:10 AM   #1
SD2010Bioinfo
Junior Member
 
Location: china

Join Date: Sep 2012
Posts: 9
Lightbulb GATKv2 UnifiedGenotyper SNP heterozygosity are extremely high!!!

When I use GATK UnifiedGenotyper to call SNP, I found that in the vcf files, ABHom SNPs are much higher(bigger than 5 times) than ABHet SNPs which is so abnormal. The following are the parameters I set.
GATK_UnifiedGenotype::java -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -l INFO -R ucsc.hg19.fasta -T UnifiedGenotyper -glm BOTH -nt 8 -A AlleleBalance -A DepthOfCoverage -A HaplotypeScore -stand_call_conf 50 -stand_emit_conf 10 --dbsnp dbsnp_135.hg19.vcf -dcov 50 -L **
GATK_VariantRecalibrator_SNP::java -Xmx4g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T VariantRecalibrator -R ucsc.hg19.fasta -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf -resourcemni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_135.hg19.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -mode SNP
GATK_VariantRecalibrator_INDEL::java -Xmx4g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T VariantRecalibrator -R ucsc.hg19.fasta -resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -an QD -an FS -an HaplotypeScore -an ReadPosRankSum -mode INDEL --maxGaussians 4
GATK_ApplyRecalibration::java -Xmx3g -jar GenomeAnalysisTK-2.1-8/GenomeAnalysisTK.jar -T ApplyRecalibration -R ucsc.hg19.fasta --ts_filter_level 99.0

Does anyone encounter the same question as me? Thank you very much!
SD2010Bioinfo is offline   Reply With Quote
Reply

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 07:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO