Daniel:Notebook/Haplotyping/2014-8-18
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Microfluidics Data[edit]
Variant Recalibration (From 8/17/2014)[edit]
Yesterday's run resulted in the same error, that there were too few variants. Since there is plenty of training data now, with the inclusion of 1000 Genomes and dbSNP, I can only assume this means I need to use more actual data. So I'm going to use all 24 chambers at once for recalibration. I may need to play with some of the options in order to make it so the files aren't merged. For now, here is the original command:
java -Xmx2g -jar /home/kunzhang/softwares/GenomeAnalysisTK-latest/GenomeAnalysisTK.jar \ -T VariantRecalibrator \ -R /media/Ext12T/GenomeDB/HsGenome/resources/human_g1k_v37.fasta \ -input Indx09/Indx09.snp.raw.vcf \ -input Indx10/Indx10.snp.raw.vcf \ -input Indx11/Indx11.snp.raw.vcf \ -input Indx12/Indx12.snp.raw.vcf \ -input Indx13/Indx13.snp.raw.vcf \ -input Indx14/Indx14.snp.raw.vcf \ -input Indx15/Indx15.snp.raw.vcf \ -input Indx16/Indx16.snp.raw.vcf \ -input Indx17/Indx17.snp.raw.vcf \ -input Indx18/Indx18.snp.raw.vcf \ -input Indx19/Indx19.snp.raw.vcf \ -input Indx20/Indx20.snp.raw.vcf \ -input Indx21/Indx21.snp.raw.vcf \ -input Indx22/Indx22.snp.raw.vcf \ -input Indx23/Indx23.snp.raw.vcf \ -input Indx24/Indx24.snp.raw.vcf \ -input Indx25/Indx25.snp.raw.vcf \ -input Indx26/Indx26.snp.raw.vcf \ -input Indx27/Indx27.snp.raw.vcf \ -input Indx28/Indx28.snp.raw.vcf \ -input Indx29/Indx29.snp.raw.vcf \ -input Indx30/Indx30.snp.raw.vcf \ -input Indx31/Indx31.snp.raw.vcf \ -input Indx32/Indx32.snp.raw.vcf \ -resource:bac,known=false,training=true,truth=false,prior=12.0 pgp1_variants_bac_all.vcf \ -resource:cgenomics,known=true,training=false,truth=true,prior=15.0 pgp1.vcf \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000Genome.chip.b36.filtered.vcf \ -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbSNP_135.no1000GProduction.vcf \ -an MQ -an HaplotypeScore -an QD -an FS -an MQRankSum -an ReadPosRankSum \ -mode SNP \ -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 95.0 -tranche 90.0 \ -recalFile recal.pgp21.recal \ -tranchesFile tranches.pgp21.tranches \ -rscriptFile rscript.pgp21.plots.R