diff --git a/scripts/getSummary.sh b/scripts/getSummary.sh index 3c827c2..0a707a7 100755 --- a/scripts/getSummary.sh +++ b/scripts/getSummary.sh @@ -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 @@ -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