NGS 102 --- Day 3

java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -R human_g1k_v37.fasta -T VariantsToTable -V intermediates/output.recalibrated.filtered.vcf -F POS -F QD -F FILTER -F MQ -F HET -F HOM-VAR -F REF -F ALT -o results.table -L 1 -raw

NGS 102 Day 2

### 1 ### variant calling using UnifiedGenotyper
java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T UnifiedGenotyper -R human_g1k_v37.fasta -I recal_20.bam -glm BOTH -stand_call_conf 30 -stand_emit_conf 10 -o raw_ug.vcf -L 20:10000000-10001000

### 2 ### variant calling using UnifiedGenotyper with gt_mode
java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T UnifiedGenotyper -R human_g1k_v37.fasta -I recal_20.bam -L 20 -ploidy 1 -glm BOTH -stand_call_conf 30 -stand_emit_conf 10 -o raw_ug_gga.vcf -gt_mode GENOTYPE_GIVEN_ALLELES -alleles NA12878.wgs.calls.vcf

### 3 ### variant calling using HaplotypeCaller with gt_mode
java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta -I recal_20.bam -stand_emit_conf 10 -stand_call_conf 30 -o raw_hc.vcf -gt_mode DISCOVERY -L 20:10000000-1000100

### 4 ### variant calling using HaplotypeCaller with gt_mode > bam out
java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37.fasta -I recal_20.bam -stand_emit_conf 10 -stand_call_conf 30 -o raw_hc.vcf -gt_mode DISCOVERY -L 20:10000000-10001000 -bamout hc_bamout.bam


### 5 ###
java -jar GenomeAnalysisTK-2.8-1-g932cd3a/GenomeAnalysisTK.jar -T VariantRecalibrator -R human_g1k_v37.fasta -input NA12878.wgs.calls.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 resources/1000G_omni2.5.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 resources/1000G_phase1.snps.high_confidence.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 resources/dbsnp_138.b37.vcf -an DP -an QD -an FS -an MQRankSum -an ReadPosRankSum -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 -recalFile recalibrate_SNP.recal -tranchesFile recalibrate_SNP.tranches -rscriptFile recalibrate_SNP_plots.R  


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