Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • plink files to vcf conversion

    Is there anyway to convert plink (.map,.ped) files back to vcf?

    I originally converted vcf to plink format files using vcftools, applied some QC in plink and now want to call the QC'd variants using Annovar - however Annovar doesn't accept plink file format, or does it? I can't see on website. Any help/advice is appreciated

    Cheers

  • #2
    Looks like the Broad may have a solution: http://www.broadinstitute.org/gsa/wi...ing_ped_to_vcf
    Last edited by nilshomer; 11-29-2011, 06:51 PM.

    Comment


    • #3
      Hi Vanisha,

      How did you convert VCF to PED using Vcftools? I tried it, but it generated error. I really appreciate your help.

      Thanks

      Comment


      • #4
        I converted from VCF to PED format, but when I looked at the PED file, it didn't show which samples are affected or unaffected? I only got two files from the conversion, PED and MAP, I still need datfile to use in the linkage, anyone knows about it?
        Thanks a lot,

        Comment


        • #5
          you can update phenotype in plink (--pheno) and you may have to make you're own .dat file for the linkage - sorry don't know much more

          Comment


          • #6
            I am also trying to convert a VCF file to plink format using vcftools, but the process never seems to result in a plink file. For example when I enter:

            ./vcftools --vcf filename.vcf --plink

            I see:

            VCFtools - v0.1.9.0
            (C) Adam Auton 2009

            Parameters as interpreted:
            --vcf filename.vcf
            --plink

            Reading Index file.
            Building new index file.
            Scanning Chromosome: chr1
            Warning - file contains entries with the same position. These entries will be processed separately.

            Scanning Chromosome: chr2
            Scanning Chromosome: chr3
            Scanning Chromosome: chr4
            Scanning Chromosome: chr5
            Scanning Chromosome: chr6
            Scanning Chromosome: chr7
            Scanning Chromosome: chr8
            Scanning Chromosome: chr9
            Scanning Chromosome: chr10
            Scanning Chromosome: chr11
            Scanning Chromosome: chr12
            Scanning Chromosome: chr13
            Scanning Chromosome: chr14
            Scanning Chromosome: chr15
            Scanning Chromosome: chr16
            Scanning Chromosome: chr17
            Scanning Chromosome: chr18
            Scanning Chromosome: chr19
            Scanning Chromosome: chr20
            Scanning Chromosome: chr21
            Scanning Chromosome: chr22
            Scanning Chromosome: chrX
            Scanning Chromosome: chrY
            Writing Index file.
            File contains 11725221 entries and 30 individuals.
            Applying Required Filters.
            After filtering, kept 30 out of 30 Individuals
            After filtering, kept 11725221 out of a possible 11725221 Sites
            Writing PLINK PED file ...
            PLINK: Only outputting biallelic loci.
            Segmentation fault: 11


            What is segmentation fault: 11 ? Is it the reason there is not a plink file output at the end of this process? Also, do I need to do something differently in order for this command to actually result in a plink files rather than a vcf?

            Many thanks...

            Comment


            • #7
              Try this:
              --vcf file.vcf --out file.plink --plink

              However, it might be better instead of converting vcf to plink and then doing plink analysis, just use vcftools to do the plink QC; the format will still be VCF, and then use the QC'd VCF to perform any downstream analysis

              Comment


              • #8
                Thanks for the tips!

                Comment


                • #9
                  After having made the plink files from the VCF file, I tried to split them up by chromosome in plink but encountered the following error:

                  ERROR: Locus has >2 alleles:
                  individual has genotype [ G 0 ]
                  but we've already seen [ G ] and [ A ]

                  I thought 0 indicated a monomorphic SNP. I am very confused. I suppose I could try splitting up the vcf file by chromosome in vcftools and then converting to plink, but I don't see why that would get around the above issue. Would it help to recode only biallelic SNPs to plink format instead of all biallelic loci? Is there a way to do that? Any input is appreciated!

                  Comment


                  • #10
                    I would like to convert bed to vcf .. I tried using plink.. i could not follow the tutorial.. Can anyone help me

                    Thanks

                    Comment


                    • #11
                      Its is again showing warning like:

                      plink: unknown option "--file"
                      plink: unknown option "--make-bed"

                      Comment

                      Latest Articles

                      Collapse

                      • seqadmin
                        Strategies for Sequencing Challenging Samples
                        by seqadmin


                        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                        03-22-2024, 06:39 AM
                      • seqadmin
                        Techniques and Challenges in Conservation Genomics
                        by seqadmin



                        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                        Avian Conservation
                        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                        03-08-2024, 10:41 AM

                      ad_right_rmr

                      Collapse

                      News

                      Collapse

                      Topics Statistics Last Post
                      Started by seqadmin, Yesterday, 06:37 PM
                      0 responses
                      8 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, Yesterday, 06:07 PM
                      0 responses
                      8 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-22-2024, 10:03 AM
                      0 responses
                      49 views
                      0 likes
                      Last Post seqadmin  
                      Started by seqadmin, 03-21-2024, 07:32 AM
                      0 responses
                      67 views
                      0 likes
                      Last Post seqadmin  
                      Working...
                      X