methow_steelhead

genetics of steelhead life history traits data analysis workflow is defined in methow_rad_workflow.txt

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
.DS_Store		.DS_Store
.gitattributes		.gitattributes
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
bwa_1.sh		bwa_1.sh
bwa_10.sh		bwa_10.sh
bwa_11.sh		bwa_11.sh
bwa_12.sh		bwa_12.sh
bwa_13.sh		bwa_13.sh
bwa_14.sh		bwa_14.sh
bwa_15.sh		bwa_15.sh
bwa_16.sh		bwa_16.sh
bwa_2.sh		bwa_2.sh
bwa_3.sh		bwa_3.sh
bwa_4.sh		bwa_4.sh
bwa_5.sh		bwa_5.sh
bwa_6.sh		bwa_6.sh
bwa_7.sh		bwa_7.sh
bwa_8.sh		bwa_8.sh
bwa_9.sh		bwa_9.sh
clone_filter.sh		clone_filter.sh
clone_filter_01.sh		clone_filter_01.sh
clone_filter_02.sh		clone_filter_02.sh
clone_filter_03.sh		clone_filter_03.sh
clone_filter_04.sh		clone_filter_04.sh
clone_filter_05.sh		clone_filter_05.sh
clone_filter_06.sh		clone_filter_06.sh
clone_filter_07.sh		clone_filter_07.sh
clone_filter_08.sh		clone_filter_08.sh
clone_filter_09.sh		clone_filter_09.sh
clone_filter_10.sh		clone_filter_10.sh
clone_filter_11.sh		clone_filter_11.sh
clone_filter_12.sh		clone_filter_12.sh
clone_filter_13.sh		clone_filter_13.sh
clone_filter_14.sh		clone_filter_14.sh
clone_filter_15.sh		clone_filter_15.sh
clone_filter_16.sh		clone_filter_16.sh
extractDP.sh		extractDP.sh
extractGQ.sh		extractGQ.sh
extractGT.sh		extractGT.sh
filter_methow_RAD_a.sh		filter_methow_RAD_a.sh
filter_methow_RAD_b.sh		filter_methow_RAD_b.sh
filter_methow_RAD_c.sh		filter_methow_RAD_c.sh
genoStats_methow_RAD.sh		genoStats_methow_RAD.sh
genome_db.sh		genome_db.sh
genotype_gvcfs.sh		genotype_gvcfs.sh
haplotypeCaller_1.sh		haplotypeCaller_1.sh
haplotypeCaller_2.sh		haplotypeCaller_2.sh
haplotypeCaller_3.sh		haplotypeCaller_3.sh
haplotypeCaller_4.sh		haplotypeCaller_4.sh
haplotypeCaller_5.sh		haplotypeCaller_5.sh
haplotypeCaller_6.sh		haplotypeCaller_6.sh
haplotypeCaller_7.sh		haplotypeCaller_7.sh
haplotypeCaller_8.sh		haplotypeCaller_8.sh
hardy.sh		hardy.sh
indexBams.sh		indexBams.sh
indexBams_1.sh		indexBams_1.sh
indexBams_2.sh		indexBams_2.sh
indexBams_3.sh		indexBams_3.sh
indexBams_4.sh		indexBams_4.sh
indexBams_5.sh		indexBams_5.sh
indexBams_6.sh		indexBams_6.sh
indexBams_7.sh		indexBams_7.sh
indexBams_8.sh		indexBams_8.sh
indivDepth.sh		indivDepth.sh
indivStats_methow_RAD.sh		indivStats_methow_RAD.sh
indivStats_methow_RAD_2.sh		indivStats_methow_RAD_2.sh
indivStats_methow_RAD_3.sh		indivStats_methow_RAD_3.sh
indivStats_methow_RAD_4.sh		indivStats_methow_RAD_4.sh
indivStats_methow_RAD_5.sh		indivStats_methow_RAD_5.sh
locus_stats.sh		locus_stats.sh
make_plink_bed.sh		make_plink_bed.sh
make_plink_bed_2.sh		make_plink_bed_2.sh
make_plink_bed_gemma.sh		make_plink_bed_gemma.sh
merge_vcfs.sh		merge_vcfs.sh
methow_rad_workflow.rtf		methow_rad_workflow.rtf
nano.save		nano.save
nano.save.1		nano.save.1
process_radtags.sh		process_radtags.sh
rCode_HDPLOT.R		rCode_HDPLOT.R
rCode_changeMapFileChromNames.R		rCode_changeMapFileChromNames.R
rCode_estimate_Omy5_LD_matrix.R		rCode_estimate_Omy5_LD_matrix.R
rCode_fixIDNamesInGenesisInputVCF.R		rCode_fixIDNamesInGenesisInputVCF.R
rCode_makeGenosForInversionPCA.R		rCode_makeGenosForInversionPCA.R
rCode_makeGenosForLDAnalysisOmy5.R		rCode_makeGenosForLDAnalysisOmy5.R
rCode_make_GEMMA_input_plot_data_21Feb2025.R		rCode_make_GEMMA_input_plot_data_21Feb2025.R
rCode_process_GWAS_data.R		rCode_process_GWAS_data.R
rCode_removeLowCovInds_7Jan2025.R		rCode_removeLowCovInds_7Jan2025.R
rCode_removeSNPsOnRead2_24Jan2025.R		rCode_removeSNPsOnRead2_24Jan2025.R
rCode_run_inversion_PCA.R		rCode_run_inversion_PCA.R
remove_no_phens.sh		remove_no_phens.sh
site_depth.sh		site_depth.sh
site_depth_missingness.sh		site_depth_missingness.sh
site_depth_missingness_2.sh		site_depth_missingness_2.sh
site_depth_missingness_qual.sh		site_depth_missingness_qual.sh
snpDepth_hardy.sh		snpDepth_hardy.sh
snpDepth_missingness_hardy_indivDepth.sh		snpDepth_missingness_hardy_indivDepth.sh
trim_reads.sh		trim_reads.sh

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Repository files navigation

methow_steelhead

About

Uh oh!

Releases

Packages

Uh oh!

Contributors

Uh oh!

Languages

License

martykardos-noaa/methow_steelhead

Folders and files

Latest commit

History

Repository files navigation

methow_steelhead

About

Resources

License

Uh oh!

Stars

Watchers

Forks

Releases

Packages 0

Uh oh!

Contributors

Uh oh!

Languages

Packages