Introduction to PLINK H3ABionet Course Covenant University, Nigeria

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1 UNIVERSITY OF THE WITWATERSRAND, JOHANNESBURG Introduction to PLINK H3ABionet Course Covenant University, Nigeria Scott Hazelhurst H3ABioNet funded by NHGRI grant number U41HG Wits Bioinformatics 1 Introduction ftp ftp://student:student@ get plinkdata.zip unzip plinkdata.zip OR if this fails you can say: wget unzip plinkdata.zip Data format Standard tool for manipulating genotype data others vcftools PLINK/PSEQ Plink has multiple data formats Other tools for converting to/from other formats pngu.mgh.harvard.edu/~purcell/plink/ PLINK in transition to PLINK 2 Current version of plink: 1.90b2 Previous version: 1.07 New version: Much faster Has more features Missing some features Data compatible PLINK primarily aimed at genotype data SNPs short indels Some support for CNV A leading tool for GWAS, structure analysis many other tools support format. Not appropriate for many SVs, or when great variability 1

2 PED format PED files with individuals information, MAP file with SNP information PED file One row per individual. Columns are Family ID, Individual ID Paternal ID, Maternal ID Sex (1=male; 2=female; other=unknown) Phenotype Missing: 9, 0; Control: 1; Case 2. (or QT) Pair of columns per SNP: different encodings possible HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB HCB Can be used to model family studies AFAM AFAM AFAM AFAM AFAM AFAM AFAM AFAM AFAM NB: Some commands/tools: Expect sex information by default --allow-no-sex often needed 2

3 Want phenotype data MAP file MAP file has one row per SNP Chromosome: (X, Y, XY, MT) SNP id genetic distance (morgans) base pair (which build!) Newer versions of PLINK have support for some non-human genomes 1 rs rs rs rs rs rs rs rs rs rs rs rs Binary PED format Faster, more compact FAM file: one row per individual identification information (first 6 columns of PED file). Human readable BIM file: one row per SNP. MAP file + two variants for that SNP. Human readable. BED file: one row per individual genotype information (rest of the columns of the PED file). Not human readable Don t confuse with UCSC BED format for genomic data can have both in a study BIM file 1 rs C C 1 rs A A 1 rs C C 1 rs G G 1 rs G G 1 rs T T 1 rs A G 1 rs A A 1 rs A A 1 rs T T 1 rs C C 1 rs G G 3

4 Other formats: transposed long format Not commonly used typically when you need to import from another format. May be easy to write a script that does the conversion. Transposed data tped/tfam files. tped: one row per SNP with SNP info followed by genotype of each individual; tfam: info about individuals Long format Very inefficient but may be useful in conversion MAP file FAM file LGEN file containing genotypes LGEN family ID, individual ID SNP ID two alleles A 1 rs123 A C A 2 rs28782 C G A 3 rs T T A 2 rs123 A C B 7 rs123 A C B 8 rs123 A C B 9 rs28782 C T Phenotype/Cluster file 4

5 Can have multiple phenotypes 1 PHE2 PHE3 1 PHE2 PHE3 1 PHE2 PHE3 1 PHE2 PHE3 Tri-allelic alleles PLINK can represent tri-allelic alleles Only very limited ability to analyse them Same SNP may appear several times in the MAP or BIM file Usually filter out tri-allelic alleles Often an issue when merging data sets Strandedness Different chips or experiments may record a SNP using different strand A C T G See when merge data appears to be multi-allelic PLINK reports apparently multi-allelic SNPs You can flip them create a new data set Try merge again if really multi-allelic should work Filter out remaining May incorrectly flip a few 5

Software for genome-wide association studies having multivariate responses: Introducing MAGWAS

Software for genome-wide association studies having multivariate responses: Introducing MAGWAS Chad C. Brown 1 and Alison A. Motsinger-Reif 1,2 1 Department of Statistics, 2 Bioinformatics Research Center