Use plink/seq (http://atgu.mgh.harvard.edu/plinkseq/)

Note: you need the reference allele file to have plink to specify reference allele

#!/bin/sh

# 1. have plink binary to specify reference allele

plink --noweb --bfile $plink_file --reference-allele $ref_Allele_file --make-bed --out $plink_file_modified

# 2. create plinkseq project

pseq $pseq_project new-project

#3. load plink file into plink/seq

pseq $pseq_project load-plink --file $plink_file_modified --id $plink_file_modified

#4. write out vcf file

pseq $pseq_project write-vcf | gzip > $plink_file_modified.vcf.gz

hope it helps!

I think this could help you, PGDSpider, An automated data conversion tool for connecting population genetics and genomics programs

http://www.cmpg.unibe.ch/software/PGDSpider/

This may help you:

http://bhoom.wordpress.com/2012/04/06/convert-plink-format-to-vcf/

Use plink/seq (http://atgu.mgh.harvard.edu/plinkseq/)

Note: you need the reference allele file to have plink to specify reference allele

#!/bin/sh

# 1. have plink binary to specify reference allele

plink --noweb --bfile $plink_file --reference-allele $ref_Allele_file --make-bed --out $plink_file_modified

# 2. create plinkseq project

pseq $pseq_project new-project

#3. load plink file into plink/seq

pseq $pseq_project load-plink --file $plink_file_modified --id $plink_file_modified

#4. write out vcf file

pseq $pseq_project write-vcf | gzip > $plink_file_modified.vcf.gz

hope it helps!

Thanks guys this is exactly what I needed. Your detailed explanation is particularly appreciated Mehdi.

I was already knocking on the door of using plink/seq but was looking at some older documentation and couldn't find where to get it from. I also downloaded vcftools but was getting bogged down in too many options. PGDspider looks worth a try too.

Thanks again.

Alternatively, you can simply export the data from plink in what's known as LINKAGE format files (simple text files):

plink --bfile $plink_file --recode --out $plink_file_modified --noweb

This will create two files (${plink_file_modified}.ped and ${plink_file_modified}.map) - the .ped file contains information for each individual in the original files, in the following format:

column 1: family ID

column 2: individual ID

column 3: father ID

column 4: mother ID

column 5: sex

column 6: phenotype (or case/control status)

column 7+: genotypes for all SNPs

(essentially replicating the .fam file in the original format, but adding the genotypes for each person to the appropriate line)

The .map file contains information on the markers (SNPs) in the following format:

column 1: chromosome

column 2: marker ID

column 3: genetic location (in cM)

column 4: physical location (in bp)

(essentially replicating the .bim file from the original format)

This format is arguably even easier to parse than VCF format (and there are numerous tools out there to parse LINKAGE-format data - from the long history of linkage and population-based genetics studies)...

Hope that helps!

The free Mega2 (http://watson.hgen.pitt.edu/docs/mega2_html/mega2.html) software will convert PLINK input files to a wide variety of other data formats. Of these, the Mega2 annotated format is easily readable in R (if you don't have too many markers).

I arrived a bit late, but if it helps anybody, plink can now output vcf directly

http://genome.sph.umich.edu/wiki/Minimac3_Cookbook_:_Converting_Files_to_VCF

How I can make reference allele file. Please help

It contains a list of SNP IDs and the allele to be set as A1, e.g.

rs10001 A

rs10002 T

rs10003 T

...

# for dbSNP_BUILD_ID=142 (reference=GRCh37.p13):

wget ftp://ftp.ncbi.nih.gov/snp/organisms/archive/human_9606_b142_GRCh37p13/VCF/All.vcf.gz

zcat All.vcf.gz | grep -v "^#" | cut -f 3,4 > reference_allele_GRCh37.txt

# for dbSNP_BUILD_ID=144 (reference=GRCh38.p2):

wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/All_20150603.vcf.gz

zcat All_20150603.vcf.gz | grep -v "^#" | cut -f 3,4 > reference_allele_GRCh38.txt

As Marcelo pointed out that Plink can convert to VCF file. I tried the following code and it worked pretty straight forward.

plink --bfile /path/to/yourfile --recode vcf --out /path/to/yourfile

The command will produce a new file with the suffix .vcf

Hi

I am going to creat marker LD plot (SNP and DArT) marker)

How I can do it in R?

Please let me know for input file format and procedure.

Thanks,

Reza