vcf file conversion

[jwhitaker17]

Is there a way to convert vcf files to the format required for the GRoSS package? Thank you!

[FerRacimo]

The GRoSS SNP input file format is very similar to the TreeMix input file format: it just needs 3 additional columns with information about chromosome number, position and SNP ID for each SNP. What I would recommend it to convert your VCF file to Plink format and then to TreeMix input file format (see here: https://speciationgenomics.github.io/Treemix/ for guidance), and then just add the 3 columns corresponding to the chromosome, position and SNP ID (which can be obtained from the intermediate plink *bim file). Note that the link also explains how to prune the data, which is something that is not required for GRoSS (so this can be skipped).

[jwhitaker17]

Thank you! ---------- Justine Whitaker, PhD Assistant Professor 906 East 1st Street 229 Gouaux Hall Nicholls State University Thibodaux, LA 70301 985-493-2628

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On Wed, Nov 20, 2019 at 12:18 PM Fernando Racimo ***@***.***> wrote: The GRoSS SNP input file format is very similar to the TreeMix input file format: it just needs 3 additional columns with information about chromosome number, position and SNP ID for each SNP. What I would recommend it to convert your VCF file to Plink format and then to TreeMix input file format (see here: https://speciationgenomics.github.io/Treemix/ for guidance), and then just add the 3 columns corresponding to the chromosome, position and SNP ID (which can be obtained from the intermediate plink *bim file). Note that the link also explains how to prune the data, which is something that is not required for GRoSS (so this can be skipped). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3?email_source=notifications&email_token=AMGULSTPWOH4UDGMHESDSCTQUV5ONA5CNFSM4JPEIUW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEETPFHI#issuecomment-556200605>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMGULSTDJWWOX663Z4VOE53QUV5ONANCNFSM4JPEIUWQ> .