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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?