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homozygous for alternate allele) odds(case | c.v. one person per line (although, as for --keep, fields after the 2nd column are allowed but they will be ignored).

One must combine this option with the desired analytic (e.g. The Error No File Plink.fam Exists error may be caused by windows system files damage. ADD REPLY • link written 17 months ago by bsmith030465 • 50 1 http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#mergelist ADD REPLY • link written 17 months ago by alesssia • 440 Hi Alesssia, thanks!

If a person is in the alternate phenotype file but not in the original file, that entry will be ignored. Due to the latter, we do not enforce a minimum VCF format version, but be aware that this flag is useless on fully-standards-compliant pre-v4.3 VCFs.) --vcf-half-call [mode] The current VCF standard For example, the file above could be specified as: SET_A rs10101 rs20234 rs29993 END GENE-B rs2344 rs888833 END

HINT It is possible to automatically create a set-file, given a list of Introduction

2.

Plink Fam File

However, these individuals will be dropped from any analyses (i.e. Multimarker tests Imputing haplotypes Precomputed lists Haplotype frequencies Haplotype-based association Haplotype-based GLM tests Haplotype-based TDT Haplotype imputation Individual phases 16. an odds ratio greater than 1 implies that the A1 allele increases risk).

To set a particular allele as A1, which might not be the minor allele, use the command The default missing value is -9, change this with --missing-phenotype, but it must be a numeric value still (in contrast to the main phenotype in the PED/FAM file).

For example F101 1 F1001 2_B F3033 1_A Drop this individual because of consent issues F4442 22 would be fine.

One must combine this option with the desired analytic (e.g. if a header row exists in the file), plink --file mydata --covar c.txt --covar-number 2,4-6,8

or plink --file mydata --covar c.txt --covar-name AGE,BMI-SMOKE,ALC

Note that ranges can be used In the latter case, the filename pattern should contain a '@' where the chromosome number would go, e.g. Plink Manual if the file recode.txt contained snp1 1 snp2 A then plink --file data --recodeAD --recode-allele recode.txt

would now report in the LOG file Reading allele coding list from [ recode.txt

Not all SNPs need be in the file (the SNP is left in, in this case; the order can be different, it can contain SNPs not in the data).

Genotype-based 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 Note that this only works for input for PED files (not TPED or LGEN files, and not for any output options, e.g. --recode, etc).

Note To load the PED file Press any key to continue . . .

ADD REPLY • link written 5.3 years ago by Zhshqzyc • 370 [code]Ignore it. Plink Vcf The plink.fam gives the ID, sex and phenotype information for each individual. PED files

As well as the --file command described above, PED and MAP files can be specified separately, if they have different names: plink --ped mydata.ped --map autosomal.map

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

Plink Merge

Case/control phenotypes are normally coded as control = 1, case = 2. Preliminar... Plink Fam File Similar posts • Search » Using PLINK to filter VCF files Hello, I am trying to filter a VCF file based on the R2 value that each SNP has. --pheno In Plink IBS/IBD estimation Pairwise IBD Inbreeding Runs of homozygosity Shared segments 11.

Do not try to view the .bed file however: it is a compressed file and you'll only see lots of strange characters on the screen...

NOTE Do not make any changes But I also have seen this. Is there a convert.snp.ped type of command out there. The 23andMe file format also does not always mark the boundaries of the X chromosome pseudo-autosomal region, so PLINK does not convert the chromosome code for 2-allele markers on male X Plink Allele Frequency

It can be reset by including the --missing-phenotype option: plink --file mydata --missing-phenotype 99

Other phenotypes can be swapped in by using the --pheno (and possibly --mpheno) option, which specify if SNP_B is not measured in the first file, but it is in the second, then any individuals in the first file who are not also present in the second file WGAS data). Any of the main single SNP association tests for diseases can be supplied instead of --assoc (e.g. --fisher, --test-missing, --logistic, etc).

All the above actives may result in the deletion or corruption of the entries in the windows system files. Plink Update Phenotype This format can be useful for subsequent analyses (i.e. 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,

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.

Genotypes not in the this file will be untouched. The clusters can be coded either numerically or as strings: F1 I1 A F2 I1 B F3 I1 B F4 I1 C1 F5 I1 A F6 I1 C2 F7 I1 C2 By default, --write-cluster generates a file with 'NA' in the cluster name field for all samples not in any cluster, and if such a file is reloaded with --within, they will Plink Tutorial The file format is the same as for --pheno (optional header line, FID and IID in first two columns, covariates in remaining columns).

How does it work? Do not name any SNPs to have the name END!

Sets can be overlapping. It must be a numeric value. My command PLINK --bfile basefile --merge-list allfiles.txt --make-bed --out Detected that binary PED file is v1.00 SNP-major mode * WARNING DUPLICATE MARKERS FOUND ** Duplicate marker name found: [ rs1051740 ]

plink --file mydata

where we expect two files: in this case, mydata.ped and mydata.map.

When PLINK starts it will attempt to contact the web, to check whether there is To invert every set, add the --complement-sets flag. alternate phenotype file and cluster files, for which this flag has no effect), the individual ID would need to be entered also as the family ID therefore. --no-parents

indicates that Consider, for an extreme example, the case where each fileset contains only a single SNP, and that there are thousands of these files -- this option would help build a single

Check your MAP files. so that input and output files can have different missing codes; this also applies to the phenotype with --output-missing-phenotype and --missing-phenotype).

The --make-bed option does the same as --recode but to select low-quality SNPs only). When using PLINK on a machine with no, or a very slow, web connection, it may be desirable to turn this feature off.

plink --file mydata --map3

In this case, the three columns are expected to be chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Base-pair position (bp units) Similarly, --vcf-min-gp excludes all genotype calls with GP value below the given threshold, assuming GP is 0-1 scaled rather than phred-scaled. (This convention will probably be in the VCFv4.3 specification, and Top teb Posts: 2 Joined: Mon Jan 14, 2013 10:33 pm Re: readin PLINK files with extensions .bed, .bim, .fam Quote Postby teb » Tue Jan 22, 2013 4:00 pm Thanks

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