Daniel:Notebook/Haplotyping/2014-8-17

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Microfluidic Data[edit]

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Variant Recalibration (From 8/14/2014)[edit]

I added data available from GATK, taken from the 1000 Genomes project and from dbSNP. The modified 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 \
-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