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Daniel:Notebook/Haplotyping/2014-1-27
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=GATK Merging vcf files= [[Daniel:Notebook/Haplotyping|Back to Calendar]] ==Creating PGP1 Vcf File== Our collaborators need a vcf file for PGP1, so I'm making one. Right now we have all the vcf files by chromosome, except chromosome 2 for some reason... ===Create Chromosome 2 vcf=== This is available in the directory: /home/kunzhang/genomeSeq/Data/RL_iPSCs_full_data/multi_GATK_calls/Feb2013_vcf '''Merge Chromosome 2 vcfs''' java -Xmx2g -jar /home/kunzhang/softwares/GenomeAnalysisTK-latest/GenomeAnalysisTK.jar -R /media/Ext12T/GenomeDB/HsGenome/resources/human_g1k_v37.fasta -T CombineVariants --variant RL_hiPSC_chr2_0.snp.snp.GATK_New.filtered.vcf --variant RL_hiPSC_chr2_45000000.snp.snp.GATK_New.filtered.vcf --variant RL_hiPSC_chr2_90000000.snp.snp.GATK_New.filtered.vcf --variant RL_hiPSC_chr2_135000000.snp.snp.GATK_New.filtered.vcf --variant RL_hiPSC_chr2_180000000.snp.snp.GATK_New.filtered.vcf --variant RL_hiPSC_chr2_225000000.snp.snp.GATK_New.filtered.vcf -o RL_hiPSC_chr2.snp.GATK_New.filtered.vcf & ===Merge PGP1 vcf files=== '''Merge PGP1 vcf files''' java -Xmx2g -jar /home/kunzhang/softwares/GenomeAnalysisTK-latest/GenomeAnalysisTK.jar -R /media/Ext12T/GenomeDB/HsGenome/resources/human_g1k_v37.fasta -T CombineVariants --variant PGP1_BacPools_chr1.bam.snp.GATK_New.filtered.vcf --variant RL_hiPSC_chr2.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr3_21.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr4_22.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr5_19.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr6_20.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr7_18.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr8_17.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr9_16.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr10_15.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr11_14.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chr12_13.bam.snp.GATK_New.filtered.vcf --variant PGP1_BacPools_chrX_Y.bam.snp.GATK_New.filtered.vcf -o PGP1_BacPoos_All.bam.snp.GATK_New.filtered.vcf
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