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Update getSummary.sh; ; removed "eval $HP_FRULE" #9

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Update getSummary.sh; ; removed "eval $HP_FRULE" #9

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14 changes: 11 additions & 3 deletions scripts/getSummary.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -28,12 +28,17 @@ V=$HP_V
awk '{print $3}' $HP_IN | sed "s|$|.cvg.stat|" | xargs cat | uniq.pl -i 0 > $ODIR/cvg.tab

#March 7th 2023
awk '{print $3}' $HP_IN | sed "s|$|.$S.00.vcf|" | xargs cat | grep -v "^##sample=" | uniq.pl | bedtools sort -header | eval $HP_FRULE > $ODIR/$S.00.concat.vcf
#awk '{print $3}' $HP_IN | sed "s|$|.$S.00.vcf|" | xargs cat | grep -v "^##sample=" | uniq.pl | bedtools sort -header | eval $HP_FRULE > $ODIR/$S.00.concat.vcf
#if [ $V ] ; then awk '{print $3}' $HP_IN | sed "s|$|.$V.00.vcf|" | xargs cat | uniq.pl | bedtools sort -header | eval $HP_FRULE > $ODIR/$V.00.concat.vcf ; fi

#Sept 22 2023
awk '{print $3}' $HP_IN | sed "s|$|.$S.00.vcf|" | xargs cat | grep -v "^##sample=" | uniq.pl | bedtools sort -header > $ODIR/$S.00.concat.vcf
if [ $V ] ; then awk '{print $3}' $HP_IN | sed "s|$|.$V.00.vcf|" | xargs cat | uniq.pl | bedtools sort -header > $ODIR/$V.00.concat.vcf ; fi

snpSort.sh $ODIR/$S.00.concat
cat $ODIR/$S.00.concat.vcf | grep -v "^#" | sed 's|:|\t|g' | count.pl -i -1 -round 100| sort -n > $ODIR/$S.00.AF.histo

if [ $V ] ; then awk '{print $3}' $HP_IN | sed "s|$|.$V.00.vcf|" | xargs cat | uniq.pl | bedtools sort -header | eval $HP_FRULE > $ODIR/$V.00.concat.vcf ; fi


#haplogroups
if [ "$HP_O" == "Human" ] ; then
Expand Down Expand Up @@ -69,7 +74,10 @@ if [ $S == "mutserve" ] ; then exit 0 ; fi

SS=$S.$S
awk '{print $3}' $HP_IN | sed "s|$|.$S.cvg.stat|" | xargs cat | uniq.pl -i 0 > $ODIR/$S.cvg.tab
awk '{print $3}' $HP_IN | sed "s|$|.$SS.00.vcf|" | xargs cat | grep -v "^##sample=" | grep -v "^##bcftools_annotateCommand" | uniq.pl | bedtools sort -header | eval $HP_FRULE > $ODIR/$SS.00.concat.vcf
#Sept 22 2023

#awk '{print $3}' $HP_IN | sed "s|$|.$SS.00.vcf|" | xargs cat | grep -v "^##sample=" | grep -v "^##bcftools_annotateCommand" | uniq.pl | bedtools sort -header | eval $HP_FRULE > $ODIR/$SS.00.concat.vcf
awk '{print $3}' $HP_IN | sed "s|$|.$SS.00.vcf|" | xargs cat | grep -v "^##sample=" | grep -v "^##bcftools_annotateCommand" | uniq.pl | bedtools sort -header > $ODIR/$SS.00.concat.vcf

snpSort.sh $ODIR/$SS.00.concat
cat $ODIR/$SS.00.concat.vcf | grep -v "^#" | sed 's|:|\t|g' | count.pl -i -1 -round 100| sort -n > $ODIR/$SS.00.AF.histo
Expand Down