R scripts to filter Genotyping by Sequencing data from the TASSEL pipeline
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.gitignore
BVZ0039-GC03L-C01~fullres-area.csv
BrachyWGSLD
Brachy_META_NO_NAs.txt
Brachypodium_META_Data.txt
Brachypodium_Species_ID.R
Diuris_Indiv-info.txt
Diuris_hmn_cleaningFig.R
GBSdombinEuc.R
GBSdominantBinDist
GWASRiyan.R
LuBrachyCA.R
LuBrachyCA.txt
Peli.R
README
SFP.R
Streichj_PhD_ANU_BorevitzLab_Genotyping_Bdistachyon.R
Streichj_PhD_ANU_BorevitzLab_Genotyping_Bhybridum.R
Streichj_PhD_ANU_BorevitzLab_Genotyping_Bstacei.R
Streichj_PhD_ANU_BorevitzLab_Genotyping_Bstacei.R .R
WheatSBSRILgenotyping.R
crosscheck_samples.R
kmeansDistachyon.txt.zip
kmeansHybridumD.txt.zip
kmeansHybridumH.txt.zip
kmeansHybridumS.txt.zip
myGBSGenos_D.txt.gz
myGBSGenos_S.txt.gz
setup_libs.R
streichj_Stacei_hapmap.txt
tassel_allele_correlation.R
tassel_create_gps_table.R
tassel_create_tree.R
tassel_fasta_to_csv.R
tassel_filter_hapmap.R
tassel_hmn_to_tagseq.R

README

README:



File Path

tassel_fasta_to_csv.R --args <tassel.fas.txt> <prefix>  -> <prefix.fas.csv>
tassel_hmn_to_tagseq.R --args <tassel.hmn.txt> <prefix.fas.csv> <prefix> -> <prefix.hmnfas.csv>
tassel_filter_hapmap.R --args <prefix.hmnfas.csv> <sample.name.csv> <prefix> -> <prefix.filtered.csv> + graphics
tassel_create_tree.R --args <prefix.filtered.csv> <prefix> -> <prefix.phylogroups.csv> + tree graphics
tassel_create_gps_table.R --args <prefix.filtered.csv> <prefix.phylogroups.csv> <prefix.names.csv> <prefix> -> <prefix.gps.csv>

crosscheck_samples.R --args <prefix.filtered.csv> <prefix>