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SelectVariants quick question about concordance/discordance

myoglumyoglu Posts: 39Member
edited November 2013 in Ask the GATK team

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?


Post edited by Geraldine_VdAuwera on

Best Answer


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