Mercurial > repos > gandres > vcftools_filter_stats_diversity

comparison 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
comparison
equal deleted inserted replaced
6:1420a55ca72b 7:ca045c1d5fa5
14 if [ "$group" != "none" ] 14 if [ "$group" != "none" ]
15 then fileout_fst=${9} 15 then fileout_fst=${9}
16 fileout_fst_marker=${10} 16 fileout_fst_marker=${10}
17 fileout_taj_combined=${11} 17 fileout_taj_combined=${11}
18 fileout_windowed_combined=${12} 18 fileout_windowed_combined=${12}
19 fileout_tstv_combined=${13}
20 fileout_snp_combined=${14}
19 fi 21 fi
20 22
21 23
22 cp $filein ${filein}.vcf 24 cp $filein ${filein}.vcf
23 if [ "$group" != "none" ] 25 if [ "$group" != "none" ]
34 if [ "$group" != "none" ] 36 if [ "$group" != "none" ]
35 then mv ${fileout_label}.fst.txt ${fileout_fst} 37 then mv ${fileout_label}.fst.txt ${fileout_fst}
36 mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker} 38 mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker}
37 mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined} 39 mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined}
38 mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined} 40 mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined}
41 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}
42 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}
39 fi 43 fi
40 44
41 rm -f ${filein}.vcf ${filein}.vcf.* 45 rm -f ${filein}.vcf ${filein}.vcf.*
42 46