Changes between Version 11 and Version 12 of DataConcordance
- Timestamp:
- Apr 21, 2011 4:43:30 PM (14 years ago)
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DataConcordance
v11 v12 8 8 * BGI Sequence data 9 9 10 = Methods & Tools=11 == File Types==10 == Methods & Tools == 11 === File Types === 12 12 All data sets were either generated or converted to VCF files aligned on the build Hg19 of the Human Reference Genome: 13 13 … … 15 15 * See [https://www.broad.harvard.edu/gsa/wiki/index.php/LiftOverVCF.pl GATK LiftOverVCF] about how to liftover a VCF file from one reference to another 16 16 17 == Concordance calculation using [http://vcftools.sourceforge.net/ VCFTools]==17 === Concordance calculation using [http://vcftools.sourceforge.net/ VCFTools] === 18 18 To calculate the concordance between the different files, [http://vcftools.sourceforge.net/ VCFTools] was used. More specifically: <pre>vcftools --vcf /data/lfrancioli/immunochip/hg19/GvNL.hg19.final.vcf --indv ${sample} --diff /data/lfrancioli/results/pilot/${sample}.human_g1k_v37.immuno.vcf --diff-site-discordance --diff-indv-discordance --diff-discordance-matrix</pre> This computes the concordance per file, site and individual as well as a discordance matrix. This was applied on a sample level so only the file, site and discordance matrix where actually used. 19 19 20 == Concordance aggregation using home-made scripts==20 === Concordance aggregation using home-made scripts === 21 21 The output of the VCFTools being per sample, they are useful for single individual QC but not for population level QC. A few scripts were developed in order to easily aggregate the data over a selection of samples files. 22 22 23 === vcftools-diff_site-concordance.pl===23 ==== vcftools-diff_site-concordance.pl ==== 24 24 As its name suggests, this script runs over the individual .diff.site files produced by VCFTools and aggregate their information. The following features are available: 25 25 … … 32 32 ** SNP filtering ** Addition of MAF from a plink frq files ** Addition of SNP ID from a plink bim file ** Output of shared SNPs only 33 33 34 === vcftools-discordance-matrix.py===34 ==== vcftools-discordance-matrix.py ==== 35 35 This script aggregates the discordance matrix files produced by vcftools into one. 36 36 37 == Reporting using R scripts==37 === Reporting using R scripts === 38 38 For reporting purpose, R scripts were created. These scripts all take files created using vcftools-diff_site-condordance.pl or vcftools-discordance-matrix.py as input. The following scripts are available: 39 39 … … 50 50 ** Plots the genotype discordance by "discordance type" (0/0 -> 0/1, 0/0 -> 1/1, 0/1 -> 0/0, etc.) ** Usage: Rscript plot_discordance_matrix.R <discordance_matrix_file> <out_plot.jpg> [dataset1_name] [dataset2_name] [show_concordant_data=FALSE] [<concordance_file>] ** Note: *** The last optional argument is a concordance file over the same data to plot as 'unknown' all loci that were not captured by the concordance matrix since the alleles were not exact matches (e.g. if one of the allele was monomorphic in one set). 51 51 52 = Results - GoNL Pilot=53 == Groningen / BGI==52 == Results - GoNL Pilot == 53 === Groningen / BGI === 54 54 Datasets: 55 55 … … 62 62 ** Produced using BGI pipeline on b36, then lifted over to hg19 ** SNPs filtered using standard BGI filter setup 63 63 64 === Loci Concordance===64 ==== Loci Concordance ==== 65 65 Below is a chart showing the shared and unique SNPs in the two datasets regardless of their genotypes. As expected, the vast majority of the SNPs are shared between the datasets, a relatively high number of SNPs are only found in Groningen (amongst them a majority of unfiltered false positives) and a small number of SNPs unique to the BGI dataset (to be investigated). 66 66 … … 69 69 After investigation, the three least concordant individuals encountered a problem while processing one of their lanes, thus leading to 2/3 of the normal coverage. The figures should be updated when the lanes have been processed and these individuals corrected. 70 70 71 === Genotype Concordance===71 ==== Genotype Concordance ==== 72 72 The following chart shows the genotype concordance on the shared SNPs between BGI and Groningen datasets. 73 73 … … 76 76 Note: The chart above does not take sex chromosomes into account as an artifact introduced by the way the Y-chrom was mapped by BGI was showing all males as completely discordant over the sex chromosomes. 77 77 78 == Groningen / Immunochip==78 === Groningen / Immunochip === 79 79 Datasets: 80 80 … … 87 87 ** ~165K loci after QC (both SNPs and homozygous reference) *** SNP HWE p-val > 1e-3 *** SNP callrate > 99% ** Exported from Genome Studio, QC'ed and lifted over from hg18 to hg19 88 88 89 === Genotype Concordance===89 ==== Genotype Concordance ==== 90 90 The following chart shows the genotype concordance on the 165K Immunochip loci left after QC. 91 91 … … 103 103 [[Image(pilot.immuno.seq.gen.concordance.test.jpg)]] 104 104 105 == BGI / Immunochip==105 === BGI / Immunochip === 106 106 Datasets: 107 107 … … 114 114 ** ~165K loci after QC (both SNPs and homozygous reference) *** SNP HWE p-val > 1e-3 *** SNP callrate > 99% ** Exported from Genome Studio, QC'ed and lifted over from hg18 to hg19 115 115 116 === Genotype Concordance===116 ==== Genotype Concordance ==== 117 117 The following chart shows the concordance between the 2 datasets over ~47K shared loci. 118 118
