Daniel:Notebook/Haplotyping/2014-8-14
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Microfluidic Data
Variant Comparison: BacPools ([[Daniel:Notebook/Haplotyping/2014-8-13|From 8/13/2014
It took a while to combine vcfs, but now I have all the .vcfs from the bacpool data merged into a single .vcf. This will now be used to compare against the microfluidic data. Ideally, we should see high concordance between the .vcfs. To compare, I ran the following command in GATK:
java -Xmx2g -jar /home/kunzhang/softwares/GenomeAnalysisTK-latest/GenomeAnalysisTK.jar \ -T VariantEval \ -R /media/Ext12T/GenomeDB/HsGenome/resources/human_g1k_v37.fasta \ -o output.eval.pgp1.bacpools.report \ --eval:Indx09 Indx09/Indx09.snp.raw.vcf \ --eval:Indx10 Indx10/Indx10.snp.raw.vcf \ --eval:Indx11 Indx11/Indx11.snp.raw.vcf \ --eval:Indx12 Indx12/Indx12.snp.raw.vcf \ --eval:Indx13 Indx13/Indx13.snp.raw.vcf \ --eval:Indx14 Indx14/Indx14.snp.raw.vcf \ --eval:Indx15 Indx15/Indx15.snp.raw.vcf \ --eval:Indx16 Indx16/Indx16.snp.raw.vcf \ --eval:Indx17 Indx17/Indx17.snp.raw.vcf \ --eval:Indx18 Indx18/Indx18.snp.raw.vcf \ --eval:Indx19 Indx19/Indx19.snp.raw.vcf \ --eval:Indx20 Indx20/Indx20.snp.raw.vcf \ --eval:Indx21 Indx21/Indx21.snp.raw.vcf \ --eval:Indx22 Indx22/Indx22.snp.raw.vcf \ --eval:Indx23 Indx23/Indx23.snp.raw.vcf \ --eval:Indx24 Indx24/Indx24.snp.raw.vcf \ --eval:Indx25 Indx25/Indx25.snp.raw.vcf \ --eval:Indx26 Indx26/Indx26.snp.raw.vcf \ --eval:Indx27 Indx27/Indx27.snp.raw.vcf \ --eval:Indx28 Indx28/Indx28.snp.raw.vcf \ --eval:Indx29 Indx29/Indx29.snp.raw.vcf \ --eval:Indx30 Indx30/Indx30.snp.raw.vcf \ --eval:Indx31 Indx31/Indx31.snp.raw.vcf \ --eval:Indx32 Indx32/Indx32.snp.raw.vcf \ --comp pgp1_variants_bac_all.vcf \ --mergeEvals