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.
SelectVariants quick question about concordance/discordance
This is my code:
java -Xmx4g -jar GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar \ -R genome.fa \ --filter_reads_with_N_cigar \ -T CombineVariants \ -V:NORMALSpost RNA-edit_SNPs_NORMALS-post_SNPeff_VA.vfc \ -V:OMNI 1000G_omni2.5.hg19.vcf \ -V:db137 dbsnp_137.hg19.vcf \ -V:Hapmap hapmap_3.3.hg19.vcf \ -V:ESP1,VCF ESP6500SI-V2-SSA137.updatedRsIds.Allchr.snps_indels_FIX.vcf \ --out NORMALS-post_TruePositives_raw.vcf && java -Xmx4g -jar GenomeAnalysisTK.jar \ -R genome.fa \ --filter_reads_with_N_cigar \ -T SelectVariants \ -V NORMALS-post_TruePositives_raw.vcf \ -select "set == 'NORMALSpost'" \ --out NORMALS-post_TruePositives.vcf
I hope I got this right: I now have SNPs (I have only called SNPs, not indels) that is found in my sample, 1000G, dbSNP and ESP. Right?
Can I easily make a VCF with all SNPs in MY sample only, not found in anything else by tweaking this code? Or must I do it some way else?