Mercurial > repos > gandres > vcftools_filter_stats_diversity

diff VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh @ 7:ca045c1d5fa5 draft

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planemo upload
author gandres
date Thu, 31 Mar 2016 10:41:59 -0400
parents b762ecbe2314
children 2b6bb9d5e4e9
line wrap: on
line diff
--- a/VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh	Mon Mar 21 10:22:36 2016 -0400
+++ b/VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh	Thu Mar 31 10:41:59 2016 -0400
@@ -16,6 +16,8 @@
 	fileout_fst_marker=${10}
 	fileout_taj_combined=${11}
 	fileout_windowed_combined=${12}
+	fileout_tstv_combined=${13}
+	fileout_snp_combined=${14}
 fi
 
 
@@ -36,6 +38,8 @@
 mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker} 
 mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined} 
 mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined}
+paste ${fileout_label}.Pop1.TsTv ${fileout_label}.Pop2.TsTv | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{$3="Pop1";$4="Pop2"}1' > ${fileout_tstv_combined}
+paste ${fileout_label}.Pop1.snpden ${fileout_label}.Pop2.snpden | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{$3="Pop1";$4="Pop2"}1' > ${fileout_snp_combined}
 fi
 
 rm -f ${filein}.vcf ${filein}.vcf.*