If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

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.

Indel Variant recalibration

Good day.
This may be a silly question, however, I wanted to know if there are any additional -known .vcf files that one must include while building the VQSR model in INDEL mode? By this I mean the "1000G_phase1.indels.hg19.vcf" and/or "Mills_and_1000G_gold_standard.indels.hg19.vcf" file.

The command currently reads as follows:
java -jar /usr/local/GenomeAnalysisTK-2.4-9/GenomeAnalysisTK.jar -nt 8 -T VariantRecalibrator -R /path/to/GRCGalaxyDatabase/H.sapiens/gatk_resource_bundle/2.3/hg19/ucsc.hg19.fasta -input indel.raw.vcf --maxGaussians 4 -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 /path/to/GRCGalaxyDatabase/H.sapiens/gatk_resource_bundle/2.3/hg19/hapmap_3.3.hg19.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 /path/to/GRCGalaxyDatabase/H.sapiens/gatk_resource_bundle/2.3/hg19/1000G_omni2.5.hg19.vcf -resource:dbsnp,VCF,known=true,training=false,truth=false,prior=6.0 /path/to/GRCGalaxyDatabase/H.sapiens/gatk_resource_bundle/2.3/hg19/dbsnp_137.hg19.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an HRun -an FS -an MQ -mode INDEL -recalFile indel.recal -tranchesFile indel.tranches -rscriptFile indel.plots.R

I thank you in advance.


Best Answer


Sign In or Register to comment.