#### Nikelski, E., Rubtsov, A. S., & Irwin, D. (2024). A sex chromosome polymorphism maintains divergent plumage phenotypes between extensively hybridizing yellowhammers (Emberiza citrinella) and pine buntings (E. leucocephalos). Molecular Ecology, in press ####

#This script contains the necessary code to complete the admixture analyses described in the above publication. The files necessary to complete these analyses as well as the directory structure of files used are documented in a previous Dryad repository (https://doi.org/10.5061/dryad.tmpg4f538). From this repository, the following files are necessary to complete the following analyses:

# GBS barcode files: GBS_Plate#_Barcode.txt
# GBS read processing file: GBS_Reads_processing_to_VCF.txt

#Raw DNA reads are available from the NCBI Sequence Read Archive under Bioproject PRJNA768601.

######Admixture analyses

cd ~/Emberiza_seq/

####Create a list of the GVCFs that will be combined for admixture.

cat > extras/Emberiza_All_Plates.Admixture.gvcf.list

----
--variant gvcf/Emberiza_GBS1_ASR00_01.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_14.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_17.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_18.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_33.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_35.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_36.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_37.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_43.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_45.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_47.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_54.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_55.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_56.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_59.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_61.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_66.g.vcf
--variant gvcf/Emberiza_GBS1_ASR05_68.g.vcf
--variant gvcf/Emberiza_GBS1_AWH_067.g.vcf
--variant gvcf/Emberiza_GBS1_AWH_076.g.vcf
--variant gvcf/Emberiza_GBS1_AWH_077.g.vcf
--variant gvcf/Emberiza_GBS1_AWH_148.g.vcf
--variant gvcf/Emberiza_GBS1_AWH_169.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1572.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1646.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1821.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1841.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1928.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1945.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1957.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1988.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_1989.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_2040.g.vcf
--variant gvcf/Emberiza_GBS1_BKS_2041.g.vcf
--variant gvcf/Emberiza_GBS1_CDS_4883.g.vcf
--variant gvcf/Emberiza_GBS1_CDS_4906.g.vcf
--variant gvcf/Emberiza_GBS1_DAB_296.g.vcf
--variant gvcf/Emberiza_GBS1_DAB_297.g.vcf
--variant gvcf/Emberiza_GBS1_ENP05_06.g.vcf
--variant gvcf/Emberiza_GBS1_ENP05_08.g.vcf
--variant gvcf/Emberiza_GBS1_ENP05_14.g.vcf
--variant gvcf/Emberiza_GBS1_ENP05_16.g.vcf
--variant gvcf/Emberiza_GBS1_ENP05_20.g.vcf
--variant gvcf/Emberiza_GBS1_ENP05_22.g.vcf
--variant gvcf/Emberiza_GBS1_ENP05_25.g.vcf
--variant gvcf/Emberiza_GBS1_ENP97_11.g.vcf
--variant gvcf/Emberiza_GBS1_ENP97_12.g.vcf
--variant gvcf/Emberiza_GBS1_ENP97_25.g.vcf
--variant gvcf/Emberiza_GBS1_EVN_327.g.vcf
--variant gvcf/Emberiza_GBS1_EVN_331.g.vcf
--variant gvcf/Emberiza_GBS1_EVN_357.g.vcf
--variant gvcf/Emberiza_GBS1_EVN_363.g.vcf
--variant gvcf/Emberiza_GBS1_EVN_573.g.vcf
--variant gvcf/Emberiza_GBS1_EVN_574.g.vcf
--variant gvcf/Emberiza_GBS1_IUK_615.g.vcf
--variant gvcf/Emberiza_GBS1_IUK_631.g.vcf
--variant gvcf/Emberiza_GBS1_IVF_309.g.vcf
--variant gvcf/Emberiza_GBS1_IVF_390.g.vcf
--variant gvcf/Emberiza_GBS1_IVF_682.g.vcf
--variant gvcf/Emberiza_GBS1_JML_291.g.vcf
--variant gvcf/Emberiza_GBS1_M05_05.g.vcf
--variant gvcf/Emberiza_GBS1_MSU_N247.g.vcf
--variant gvcf/Emberiza_GBS1_MSU_N339.g.vcf
--variant gvcf/Emberiza_GBS1_MSU_P66.g.vcf
--variant gvcf/Emberiza_GBS1_NVN_015.g.vcf
--variant gvcf/Emberiza_GBS1_RCF_1807.g.vcf
--variant gvcf/Emberiza_GBS1_RCF_1971.g.vcf
--variant gvcf/Emberiza_GBS1_RCF_2235.g.vcf
--variant gvcf/Emberiza_GBS1_SVD_2134.g.vcf
--variant gvcf/Emberiza_GBS1_SVD_2695.g.vcf
--variant gvcf/Emberiza_GBS1_SVD_3479.g.vcf
--variant gvcf/Emberiza_GBS1_SVD_518.g.vcf
--variant gvcf/Emberiza_GBS1_SVD_519.g.vcf
--variant gvcf/Emberiza_GBS1_SVD_531.g.vcf
--variant gvcf/Emberiza_GBS1_SWM_03.g.vcf
--variant gvcf/Emberiza_GBS1_SWM_10.g.vcf
--variant gvcf/Emberiza_GBS1_SWM_12.g.vcf
--variant gvcf/Emberiza_GBS1_VGR_400.g.vcf
--variant gvcf/Emberiza_GBS1_VGR_440.g.vcf
--variant gvcf/Emberiza_GBS1_VGR_508.g.vcf
--variant gvcf/Emberiza_GBS1_VM_282a.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_02.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_15.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_20.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_22.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_32.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_38.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_39.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_40.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_41.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_44.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_46.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_49.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_51.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_52.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_57.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_58.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_60.g.vcf
--variant gvcf/Emberiza_GBS2_ASR05_67.g.vcf
--variant gvcf/Emberiza_GBS2_ASR98_11.g.vcf
--variant gvcf/Emberiza_GBS2_ASR98_17.g.vcf
--variant gvcf/Emberiza_GBS2_ASR99_01.g.vcf
--variant gvcf/Emberiza_GBS2_AWH_039.g.vcf
--variant gvcf/Emberiza_GBS2_AWH_152.g.vcf
--variant gvcf/Emberiza_GBS2_BKS_1583.g.vcf
--variant gvcf/Emberiza_GBS2_BKS_1609.g.vcf
--variant gvcf/Emberiza_GBS2_BKS_1654.g.vcf
--variant gvcf/Emberiza_GBS2_BKS_1667.g.vcf
--variant gvcf/Emberiza_GBS2_BKS_1710.g.vcf
--variant gvcf/Emberiza_GBS2_BKS_1859.g.vcf
--variant gvcf/Emberiza_GBS2_BKS_2017.g.vcf
--variant gvcf/Emberiza_GBS2_DAB_291.g.vcf
--variant gvcf/Emberiza_GBS2_DAB_299.g.vcf
--variant gvcf/Emberiza_GBS2_DAB_301.g.vcf
--variant gvcf/Emberiza_GBS2_DAB_303.g.vcf
--variant gvcf/Emberiza_GBS2_DAB_308.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_04.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_09.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_11.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_12.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_15.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_21.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_24.g.vcf
--variant gvcf/Emberiza_GBS2_ENP05_26.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_01.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_03.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_05.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_07.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_09.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_10.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_13.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_15.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_20.g.vcf
--variant gvcf/Emberiza_GBS2_ENP97_21.g.vcf
--variant gvcf/Emberiza_GBS2_EVN_328.g.vcf
--variant gvcf/Emberiza_GBS2_EVN_366.g.vcf
--variant gvcf/Emberiza_GBS2_EVN_570.g.vcf
--variant gvcf/Emberiza_GBS2_IUK_2343.g.vcf
--variant gvcf/Emberiza_GBS2_IUK_702.g.vcf
--variant gvcf/Emberiza_GBS2_IUK_703.g.vcf
--variant gvcf/Emberiza_GBS2_IUK_801.g.vcf
--variant gvcf/Emberiza_GBS2_M05_01.g.vcf
--variant gvcf/Emberiza_GBS2_M05_03.g.vcf
--variant gvcf/Emberiza_GBS2_M05_08.g.vcf
--variant gvcf/Emberiza_GBS2_M05_10.g.vcf
--variant gvcf/Emberiza_GBS2_MSU_N71.g.vcf
--variant gvcf/Emberiza_GBS2_RCF_1949.g.vcf
--variant gvcf/Emberiza_GBS2_RCF_1970.g.vcf
--variant gvcf/Emberiza_GBS2_RCF_2191b.g.vcf
--variant gvcf/Emberiza_GBS2_RCF_2192.g.vcf
--variant gvcf/Emberiza_GBS2_RCF_2230.g.vcf
--variant gvcf/Emberiza_GBS2_SVD_3563.g.vcf
--variant gvcf/Emberiza_GBS2_SVD_514.g.vcf
--variant gvcf/Emberiza_GBS2_SVD_524.g.vcf
--variant gvcf/Emberiza_GBS2_SVD_533.g.vcf
--variant gvcf/Emberiza_GBS2_SWM_11.g.vcf
--variant gvcf/Emberiza_GBS2_VGR_343.g.vcf
--variant gvcf/Emberiza_GBS2_VGR_350.g.vcf
--variant gvcf/Emberiza_GBS2_VGR_355.g.vcf
--variant gvcf/Emberiza_GBS2_VM_285a.g.vcf
--variant gvcf/Emberiza_GBS2_ZMUC_09.g.vcf
--variant gvcf/Emberiza_GBS4_MIM_165.g.vcf
--variant gvcf/Emberiza_GBS4_R06_01.g.vcf
--variant gvcf/Emberiza_GBS4_RYA_2397.g.vcf
--variant gvcf/Emberiza_GBS4_RYA_2680.g.vcf
--variant gvcf/Emberiza_GBS4_RYA_3178.g.vcf
--variant gvcf/Emberiza_GBS4_SVN_2335.g.vcf
--variant gvcf/Emberiza_GBS4_XD_548.g.vcf
--variant gvcf/Emberiza_GBS4_XD_552.g.vcf
--variant gvcf/Emberiza_GBS4_XD_603.g.vcf
--variant gvcf/Emberiza_GBS4_XD_610.g.vcf
--variant gvcf/Emberiza_GBS4_XD_612.g.vcf
--variant gvcf/Emberiza_GBS4_XD_613.g.vcf
--variant gvcf/Emberiza_GBS4_XD_617.g.vcf
--variant gvcf/Emberiza_GBS4_XD_619.g.vcf
--variant gvcf/Emberiza_GBS4_XD_621.g.vcf
--variant gvcf/Emberiza_GBS4_XD_623.g.vcf
--variant gvcf/Emberiza_GBS4_XD_624.g.vcf
--variant gvcf/Emberiza_GBS4_XD_625.g.vcf
--variant gvcf/Emberiza_GBS4_XD_630.g.vcf
--variant gvcf/Emberiza_GBS4_XD_631.g.vcf
--variant gvcf/Emberiza_GBS4_XD_632.g.vcf
--variant gvcf/Emberiza_GBS4_XD_634.g.vcf
--variant gvcf/Emberiza_GBS4_XD_635.g.vcf
--variant gvcf/Emberiza_GBS4_XD_636.g.vcf
--variant gvcf/Emberiza_GBS4_XD_637.g.vcf
--variant gvcf/Emberiza_GBS4_XD_639.g.vcf
--variant gvcf/Emberiza_GBS4_XD_640.g.vcf
--variant gvcf/Emberiza_GBS4_XD_645.g.vcf
--variant gvcf/Emberiza_GBS4_XD_647.g.vcf
--variant gvcf/Emberiza_GBS4_XD_649.g.vcf
--variant gvcf/Emberiza_GBS4_XD_650.g.vcf
--variant gvcf/Emberiza_GBS4_XD_653.g.vcf
--variant gvcf/Emberiza_GBS4_XD_654.g.vcf
--variant gvcf/Emberiza_GBS4_XD_655.g.vcf
--variant gvcf/Emberiza_GBS4_XD_656.g.vcf
--variant gvcf/Emberiza_GBS4_XD_657.g.vcf
--variant gvcf/Emberiza_GBS4_XD_658.g.vcf
--variant gvcf/Emberiza_GBS4_XD_659.g.vcf
--variant gvcf/Emberiza_GBS4_XD_663.g.vcf
--variant gvcf/Emberiza_GBS4_XD_666.g.vcf
--variant gvcf/Emberiza_GBS4_XD_670.g.vcf
--variant gvcf/Emberiza_GBS4_XD_672.g.vcf
--variant gvcf/Emberiza_GBS4_XD_674.g.vcf
--variant gvcf/Emberiza_GBS4_XD_684.g.vcf
--variant gvcf/Emberiza_GBS4_XD_688.g.vcf
--variant gvcf/Emberiza_GBS4_XD_699.g.vcf
--variant gvcf/Emberiza_GBS4_XD_700.g.vcf
--variant gvcf/Emberiza_GBS4_XD_792.g.vcf
--variant gvcf/Emberiza_GBS4_XD_798.g.vcf
--variant gvcf/Emberiza_GBS4_XD_800.g.vcf
--variant gvcf/Emberiza_GBS4_XD_930.g.vcf
--variant gvcf/Emberiza_GBS4_XD_934.g.vcf
--variant gvcf/Emberiza_GBS4_XD_940.g.vcf
--variant gvcf/Emberiza_GBS4_XD_941.g.vcf
--variant gvcf/Emberiza_GBS4_XD_946.g.vcf
--variant gvcf/Emberiza_GBS4_XD_947.g.vcf
--variant gvcf/Emberiza_GBS4_XD_948.g.vcf
--variant gvcf/Emberiza_GBS4_XD_949.g.vcf
--variant gvcf/Emberiza_GBS4_XD_950.g.vcf
--variant gvcf/Emberiza_GBS4_XD_957.g.vcf
--variant gvcf/Emberiza_GBS4_XD_958.g.vcf
--variant gvcf/Emberiza_GBS4_XD_960.g.vcf
--variant gvcf/Emberiza_GBS4_XD_961.g.vcf
--variant gvcf/Emberiza_GBS4_XD_962.g.vcf
--variant gvcf/Emberiza_GBS4_XD_967.g.vcf
--variant gvcf/Emberiza_GBS4_XD_968.g.vcf
--variant gvcf/Emberiza_GBS4_XD_971.g.vcf
--variant gvcf/Emberiza_GBS4_XD_972.g.vcf
--variant gvcf/Emberiza_GBS4_XD_976.g.vcf
--variant gvcf/Emberiza_GBS4_XD_977.g.vcf
--variant gvcf/Emberiza_GBS4_XD_979.g.vcf
--variant gvcf/Emberiza_GBS4_XD_990.g.vcf
--variant gvcf/Emberiza_GBS4_XD_994.g.vcf
--variant gvcf/Emberiza_GBS4_XD_995.g.vcf
--variant gvcf/Emberiza_GBS4_XD_997.g.vcf
--variant gvcf/Emberiza_GBS4_ZM_1164.g.vcf
--variant gvcf/Emberiza_GBS4_ZM_1184.g.vcf
--variant gvcf/Emberiza_GBS4_ZM_1335.g.vcf
--variant gvcf/Emberiza_GBS5_ASR05_62_2.g.vcf
--variant gvcf/Emberiza_GBS5_ENP05_02.g.vcf
--variant gvcf/Emberiza_GBS5_RYA_3003.g.vcf
--variant gvcf/Emberiza_GBS5_SVN_2336.g.vcf
--variant gvcf/Emberiza_GBS5_XD_549.g.vcf
--variant gvcf/Emberiza_GBS5_XD_550.g.vcf
--variant gvcf/Emberiza_GBS5_XD_602.g.vcf
--variant gvcf/Emberiza_GBS5_XD_605.g.vcf
--variant gvcf/Emberiza_GBS5_XD_608.g.vcf
--variant gvcf/Emberiza_GBS5_XD_609.g.vcf
--variant gvcf/Emberiza_GBS5_XD_611.g.vcf
--variant gvcf/Emberiza_GBS5_XD_615.g.vcf
--variant gvcf/Emberiza_GBS5_XD_616.g.vcf
--variant gvcf/Emberiza_GBS5_XD_620.g.vcf
--variant gvcf/Emberiza_GBS5_XD_622.g.vcf
--variant gvcf/Emberiza_GBS5_XD_626.g.vcf
--variant gvcf/Emberiza_GBS5_XD_627.g.vcf
--variant gvcf/Emberiza_GBS5_XD_628.g.vcf
--variant gvcf/Emberiza_GBS5_XD_629.g.vcf
--variant gvcf/Emberiza_GBS5_XD_633.g.vcf
--variant gvcf/Emberiza_GBS5_XD_638.g.vcf
--variant gvcf/Emberiza_GBS5_XD_642.g.vcf
--variant gvcf/Emberiza_GBS5_XD_643.g.vcf
--variant gvcf/Emberiza_GBS5_XD_646.g.vcf
--variant gvcf/Emberiza_GBS5_XD_648.g.vcf
--variant gvcf/Emberiza_GBS5_XD_651.g.vcf
--variant gvcf/Emberiza_GBS5_XD_660.g.vcf
--variant gvcf/Emberiza_GBS5_XD_661.g.vcf
--variant gvcf/Emberiza_GBS5_XD_667.g.vcf
--variant gvcf/Emberiza_GBS5_XD_668.g.vcf
--variant gvcf/Emberiza_GBS5_XD_683.g.vcf
--variant gvcf/Emberiza_GBS5_XD_685.g.vcf
--variant gvcf/Emberiza_GBS5_XD_686.g.vcf
--variant gvcf/Emberiza_GBS5_XD_687.g.vcf
--variant gvcf/Emberiza_GBS5_XD_689.g.vcf
--variant gvcf/Emberiza_GBS5_XD_690.g.vcf
--variant gvcf/Emberiza_GBS5_XD_694.g.vcf
--variant gvcf/Emberiza_GBS5_XD_698.g.vcf
--variant gvcf/Emberiza_GBS5_XD_794.g.vcf
--variant gvcf/Emberiza_GBS5_XD_795.g.vcf
--variant gvcf/Emberiza_GBS5_XD_797.g.vcf
--variant gvcf/Emberiza_GBS5_XD_799.g.vcf
--variant gvcf/Emberiza_GBS5_XD_924.g.vcf
--variant gvcf/Emberiza_GBS5_XD_925.g.vcf
--variant gvcf/Emberiza_GBS5_XD_927.g.vcf
--variant gvcf/Emberiza_GBS5_XD_928.g.vcf
--variant gvcf/Emberiza_GBS5_XD_931.g.vcf
--variant gvcf/Emberiza_GBS5_XD_942.g.vcf
--variant gvcf/Emberiza_GBS5_XD_943.g.vcf
--variant gvcf/Emberiza_GBS5_XD_944.g.vcf
--variant gvcf/Emberiza_GBS5_XD_952.g.vcf
--variant gvcf/Emberiza_GBS5_XD_954.g.vcf
--variant gvcf/Emberiza_GBS5_XD_955.g.vcf
--variant gvcf/Emberiza_GBS5_XD_956.g.vcf
--variant gvcf/Emberiza_GBS5_XD_963.g.vcf
--variant gvcf/Emberiza_GBS5_XD_964.g.vcf
--variant gvcf/Emberiza_GBS5_XD_965.g.vcf
--variant gvcf/Emberiza_GBS5_XD_966.g.vcf
--variant gvcf/Emberiza_GBS5_XD_969.g.vcf
--variant gvcf/Emberiza_GBS5_XD_970.g.vcf
--variant gvcf/Emberiza_GBS5_XD_973.g.vcf
--variant gvcf/Emberiza_GBS5_XD_974.g.vcf
--variant gvcf/Emberiza_GBS5_XD_975.g.vcf
--variant gvcf/Emberiza_GBS5_XD_978.g.vcf
--variant gvcf/Emberiza_GBS5_XD_980.g.vcf
--variant gvcf/Emberiza_GBS5_XD_981.g.vcf
--variant gvcf/Emberiza_GBS5_XD_982.g.vcf
--variant gvcf/Emberiza_GBS5_XD_983.g.vcf
--variant gvcf/Emberiza_GBS5_XD_984.g.vcf
--variant gvcf/Emberiza_GBS5_XD_985.g.vcf
--variant gvcf/Emberiza_GBS5_XD_987.g.vcf
--variant gvcf/Emberiza_GBS5_XD_989.g.vcf
--variant gvcf/Emberiza_GBS5_XD_992.g.vcf
--variant gvcf/Emberiza_GBS5_XD_993.g.vcf
--variant gvcf/Emberiza_GBS5_XD_999.g.vcf
--variant gvcf/Emberiza_GBS5_ZM_1162.g.vcf
--variant gvcf/Emberiza_GBS5_ZM_1183.g.vcf
--variant gvcf/Emberiza_GBS5_ZM_1197.g.vcf
--variant gvcf/Emberiza_GBS5_ZM_1200.g.vcf
--variant gvcf/Emberiza_GBS5_ZM_1220.g.vcf
--variant gvcf/Emberiza_GBS5_ZM_1267.g.vcf
--variant gvcf/Emberiza_GBS5_ZM_1375.g.vcf


##Put self in new screen

screen -S ADMIX

##Run GATK GenotypeGVCFs to combine all GVCFs into a single file --> only contain SNPs that separate these individuals

java -jar /Linux/GATK-3.8/GenomeAnalysisTK.jar -T GenotypeGVCFs -R ref/Taeniopygia_guttata.taeGut3.2.4.dna_rm.toplevel.fa -l INFO -V extras/Emberiza_All_Plates.Admixture.gvcf.list -o combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.vcf -log combined_vcfs_logs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.log


##Filter VCF
# Remove indels and SNPs with more than two alleles:

vcftools --vcf combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.vcf --remove-indels --max-alleles 2 --recode --recode-INFO-all --out combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.vcf

# now filter out some questionable loci using GATK:

java -jar /Linux/GATK-3.8/GenomeAnalysisTK.jar -T VariantFiltration -R ref/Taeniopygia_guttata.taeGut3.2.4.dna_rm.toplevel.fa -V combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.vcf.recode.vcf --filterExpression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || SOR > 3.0 || ReadPosRankSum < -8.0" --filterName "GATK_rec_filters" --setFilteredGtToNocall -o combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered.vcf

# The above flags the variants that PASS or don't. Now actually remove the ones that don't:

java -jar /Linux/GATK-3.8/GenomeAnalysisTK.jar -T SelectVariants -R ref/Taeniopygia_guttata.taeGut3.2.4.dna_rm.toplevel.fa -V combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered.vcf --excludeFiltered -o combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.vcf

# Remove sites with more than 60% missing genotypes (note the parameter below is intuition times minus one):

vcftools --vcf combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.vcf --max-missing 0.4 --recode --recode-INFO-all --out combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60.vcf

### DO NOT CONVERT TO 012NA format

##Move onto admixture code

###Make new directory
mkdir ADMIXTURE.2 


#### Generate Bed files
#Generate pet and map files in plink

/Linux/bin/vcftools --vcf combined_vcfs/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60.vcf.recode.vcf --plink --out ADMIXTURE.2/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60


###########Export map files to excel to change chromosome location values of 0 to correct values########### 

#trim on LD:
/Linux/bin/plink_1.9 \
--file ADMIXTURE.2/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60 \
--indep-pairwise 50 10 0.1 \
--allow-no-sex \
--allow-extra-chr \
--chr-set 28 \
--out ADMIXTURE.2/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60_LDtrim


#MAKE A BED FILE WITH THE PRUNED SNPS
/Linux/bin/plink_1.9 \
--file ADMIXTURE.2/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60 \
--extract ADMIXTURE.2/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60_LDtrim.prune.in \
--allow-no-sex \
--allow-extra-chr 0 \
--make-bed \
--chr-set 28 \
--out ADMIXTURE.2/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60_LDtrim


#Run Admixture
cd ~/Emberiza_seq/ADMIXTURE.2

cat > runadmixture2.sh

!#/bin/bash

for K in 1 2 3 4 5 6; \
do ~/Emberiza_seq/ADMIXTURE/tools/admixture_linux-1.3.0/admixture \
--cv=10 \
-s time \
-j10 \
-C 0.0000000001 \
~/Emberiza_seq/ADMIXTURE.2/Emberiza_All_Plates.genotypes.variant_only.whole_genome.ADMIX.max2allele_noindel.GATKfiltered_excluded.maxmiss60_LDtrim.bed \
$K | tee log${K}.out; \
done

chmod 755 runadmixture2.sh

screen -r ADMIX 
bash
./runadmixture2.sh

#CV error
grep -h CV log*.out
CV error (K=1): 0.18440
CV error (K=2): 0.18910
CV error (K=3): 0.19839
CV error (K=4): 0.20220
CV error (K=5): 0.20777
CV error (K=6): 0.21445