Commit c65d7278 authored by Kosmas Hench's avatar Kosmas Hench
Browse files

change in 2.2.5.4 genome wide fst pan

parent e4900339

2_reSeq-scripts/2-2_popGen/2.2.5.4.fst_gw.pan.sh

+14 −14
Original line number Diff line number Diff line
@@ -4,25 +4,25 @@ 
#PBS -l cpunum_job=1

#PBS -N fstGlobal

#PBS -q clexpress

#PBS -o 2.2.5.4.fst_gw_bel.stdout

#PBS -e 2.2.5.4.fst_gw_bel.stderr

#PBS -o 2.2.5.4.fst_gw_pan.stdout

#PBS -e 2.2.5.4.fst_gw_pan.stderr



cd $WORK/2_output/08_popGen/05_fst



vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \

	--keep $WORK/0_data/0_resources/vcfpops/vcftools_bel.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_nigbel.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_puebel.pop \

	--out fst.gw.nigbel-puebel

	--keep $WORK/0_data/0_resources/vcfpops/vcftools_boc.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_nigboc.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_pueboc.pop \

	--out fst.gw.nigboc-pueboc



vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \

	--keep $WORK/0_data/0_resources/vcfpops/vcftools_bel.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_nigbel.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_unibel.pop \

	--out fst.gw.nigbel-unibel

	--keep $WORK/0_data/0_resources/vcfpops/vcftools_boc.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_nigboc.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_uniboc.pop \

	--out fst.gw.nigboc-uniboc



vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \

	--keep $WORK/0_data/0_resources/vcfpops/vcftools_bel.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_puebel.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_unibel.pop \

	--out fst.gw.puebel-unibel
 
 No newline at end of file
 
	--keep $WORK/0_data/0_resources/vcfpops/vcftools_boc.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_pueboc.pop \

	--weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_uniboc.pop \

	--out fst.gw.pueboc-uniboc
 
 No newline at end of file