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| author | Pjotr Prins | 2021-09-22 12:53:57 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2021-09-22 12:53:57 +0200 |
| commit | c470d669152d82d810895b6a34513c6fb2a7fbf7 (patch) | |
| tree | f2108dfbfee9ad6e347ea7d6b72e2acb1c13ede1 | |
| parent | b369e3e34a7058871ade7dc8f803957e246b26eb (diff) | |
| download | gn-gemtext-c470d669152d82d810895b6a34513c6fb2a7fbf7.tar.gz | |
Track MIKK
| -rw-r--r-- | issues/data/MIKK-panel.gmi | 21 |
1 files changed, 21 insertions, 0 deletions
diff --git a/issues/data/MIKK-panel.gmi b/issues/data/MIKK-panel.gmi new file mode 100644 index 0000000..672835d --- /dev/null +++ b/issues/data/MIKK-panel.gmi @@ -0,0 +1,21 @@ +# Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel + +Genotyping from VCF + + On Tue, Sep 21, 2021 at 12:15 PM Arthur Centeno <[1]acenteno@gmail.com> + wrote: + + Hi Pjotr, + Uploading now + to /export2/local/home/acenteno/Ian_MIKK_genotypes/mikk_clean.vcf.gz + It will take a while (~14.69GB) + Arthur + + On Tue, Sep 21, 2021 at 12:03 PM Pjotr Prins <[2]pjotr2021@thebird.nl> + wrote: + + PLINK to .GENO is straightforward. We can use the tool I wrote (gemma2lib) which goes via Rqtl2. PLINK can also convert from VCF and then on to .GENO, but I think that route is nasty and probably error prone. bcftools same, same. Arthur, if you copy the VCF files to tux01 and tell me when and where, I can have a go at setting up a tool chain we/you can use. + +## Tags + +* assigned: pjotrp, acenteno |