Mercurial > repos > gandres > vcftools_filter_stats_diversity

comparison VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh @ 11:f494c8d22725 draft default tip

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planemo upload
author gandres
date Wed, 15 Jun 2016 09:40:02 -0400
parents 2b6bb9d5e4e9
children
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10:2b7eb79f0ba0 11:f494c8d22725
45 if [ "$group" != "none" ] 45 if [ "$group" != "none" ]
46 then mv ${fileout_label}.fst.txt ${fileout_fst} 46 then mv ${fileout_label}.fst.txt ${fileout_fst}
47 mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker} 47 mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker}
48 mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined} 48 mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined}
49 mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined} 49 mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined}
50 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} 50 paste ${fileout_label}.Pop1.TsTv ${fileout_label}.Pop2.TsTv | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{OFS="\t"; $3="Pop1";$4="Pop2"}1' > ${fileout_tstv_combined}
51 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} 51 paste ${fileout_label}.Pop1.snpden ${fileout_label}.Pop2.snpden | column -s $'\t' -t | awk '{OFS="\t"; print $1,$2,$4,$8} ' | awk 'NR==1{OFS="\t"; $3="Pop1";$4="Pop2"}1' > ${fileout_snp_combined}
52 fi 52 fi
53 53
54 rm -f ${filein}.vcf ${filein}.vcf.* 54 rm -f ${filein}.vcf ${filein}.vcf.*
55 55