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Plink Fam File

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Any SNPs specified in the set that do not appear in the actual data, or that have been excluded due to filters used, will be ignored.

The format is flexible perl retrieve_data.pl | ./plink --ped - --map mymap.map --make-bed

The MAP file still needs to be a normal file; this currently only works for --ped files. This maximizes similarity between the VCF and BCF2 parsers. 'missing'/'m': Treat half-calls as missing. 'reference'/'r': Treat the missing part as reference. Oxford format --data {prefix} --gen [filename] --bgen [filename] Write SNP list files

To output just the list of SNPs that remain after all filtering, etc, use the --write-snplist command, e.g.

selecting AGE, BMI, ETH, SMOKE, ALC.

To output a new covariate file, possibly with categorical variables downcoded to binary dummy variables use the --write-covar option as described here

Exception GT 0/0 ./. ./. Meta-analysis Basic usage Misc. How to create study1.assoc file format in PLINK from text file How to create study1.assoc from study1.txt in PLINK?   Thanks Merge Two Plink Transposed Files I want to look at concordance

Plink Fam File

from "how to ..." to "[SOLVED] how to ..."). It is sometimes useful to have a PED file that is tab-delimited, except that between alleles of the same genotype a space instead of a tab is used. Profile scoring Basic usage SNP subsets Dosage data Misc options 31.

Listing by long-format (LGEN) To output a file in the LGEN format, use the command --recode-lgen which generates files plink.lgen plink.fam plink.map that can be read with the --lfile command. For example, '--missing-code -9,0,NA,na' would cause '-9', '0', 'NA', and 'na' to all be interpreted as missing phenotypes. (Note that no spaces are currently permitted between the strings.) By default, only For example, the if the original contains ... Plink Manual SET_A or GENE-B in this example.

This can be combined with one or more (space-delimited) filter names to ignore. ##fileformat=VCFv4.1 ##filedate=20140317 ##source=myImputationProgramV3.14 ##FILTER= ##FILTER= ##FORMAT= ##contig= #CHROM POS Plink Merge PDF documentation 3. They're irrelevant unless you are merging with a dataset which contains known relatives. SNP_A-1919191 rs123456 SNP_A-64646464 rs222222 ...

There can be many events which may have resulted in the system files errors. Plink Vcf As described above, the --range command can modify the behaviour of --exclude in the same manner as for --extract.

One must combine this option with the desired analytic (e.g. --assoc), All the above actives may result in the deletion or corruption of the entries in the windows system files. Gene-based report Basic usage Other options 24.

Plink Merge

Inclusion thresholds Missing/person Allele frequency Missing/SNP Hardy-Weinberg Mendel errors 9. All generated samples are females with random genotype and phenotype values. Plink Fam File Rare CNVs File format MAP file construction Loading CNVs Check for overlap Filter on type Filter on genes Filter on frequency Burden analysis Geneset enrichment Mapping loci Regional tests Quantitative traits --pheno In Plink In this case, the TPED file will be very long (as opposed to the PED file being very wide).

To read a transposed fileset, use the command plink --tfile mydata

If a prefix is provided, it replaces 'plink'. --gen, --bgen, and --sample allow you to specify the filenames separately; --gen is necessary if your genomic data file has a .gen.gz extension, This feature is turned on by default so that users are aware of new versions that may contain important new features or bug fixes. the third SNP, rs0003), c) that SNPs in the reference file that are not present in the dataset (e.g. With .gen input, the first column is normally assumed to contain chromosome codes. Plink Allele Frequency

Creating a new binary phenotype automatically To automatically form a one-versus-others binary phenotype (note: binary meaning dichotomous here, rather than a BED/binary-PED file) from a categorical covariate/phenotype file, use the command This is common error code format used by windows and other windows compatible software and driver vendors. options 22. setting the position to a negative value will not work to exclude a SNP for binary files

You can specify a different output root file name (i.e.

All Rights Reserved. Plink Update Phenotype To unlock all features and tools, a purchase is required. When using a data generation command (e.g. --make-bed, --recode, etc) as opposed to an analysis command, then by default the phenotype is not set to missing is sex is missing.

The phenotype can be either a quantitative trait or an affection status column: PLINK will automatically detect which type (i.e.

Discrete calls PLINK 1 binary --bfile {prefix} The --bfile flag causes the binary fileset plink.bed + plink.bim + plink.fam to be referenced. (The structure of these files is described in the Population stratification IBS clustering Permutation test Clustering options IBS matrix Multidimensional scaling Outlier detection 10. Recode phenotype in PLINK Hi I have converted files gen/sample (using gtool) to ped/map to be used in PLINK with phenotype... Plink Tutorial A8504 1 5 0.606218 A8008 1 1 0.442154 A8542 1 7 0.388042 A8022 1 2 0.286125 A8024 1 3 0.903004 A8026 1 4 0.790778 A8524 1 -9 0.713952 A8556 1 0

Permutation procedures Basic permutation Adaptive permutation max(T) permutation Ranked permutation Gene-dropping Within-cluster Permuted phenotypes files 14. spaces Flag/parameter reuse System resource usage Pseudorandom numbers Resources 1000 Genomes phase 1 Teaching materials Gene range lists Functional SNP attributes Errors and warnings Output file list Order of operations For What syntax is your input file? "text" doesn't mean much, since lots of them appear to be text of different arrangement. As a result, if you're performing multiple operations on the same otherwise-formatted files, you may want to keep the autoconversion products and work with them, instead of repeating the conversion on

If you just want to convert your data, don't use any other flags besides --out. In this case, the file allfiles.txt was a list of the to-be-merged files, one set per row: fB.ped fB.map fC.ped fC.map fD.ped fD.map fE.bed fE.bim fE.fam fF.bed fF.bim fF.fam fG.bed fG.bim Given .ped and .map, program automatically create bim,bed,fam 3 files. Use the option --tab as well as --recode or --recode12 to achieve this effect.

To make a new file in which non-founders without both parents also in the same fileset

This can be accomplished with the --loop-assoc command, e.g. ./plink --bfile mydata --loop-assoc plate.lst --assoc

The file plate.lst should be in the same format as a cluster file, although it different to "plink") by using the --out option: plink --file mydata --out mydata --make-bed

which will create mydata.bed mydata.fam mydata.bim To subsequently load a binary file, just use --bfile instead IBS/IBD estimation Pairwise IBD Inbreeding Runs of homozygosity Shared segments 11. Thanks a lot, Suparna.

in this case, the labels remain the same, but whether the minor allele is A or T will still depend on strand).

To flip strand for just a subset of plink --file data --extract myrange.txt --range

All SNPs within that range will then be excluded or extracted.