Originally posted by KaiYe
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Thanks,
Boel
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cat XXXX_D.vcf | grep DEL | awk '{print $1,"\t",$2,"\t&&&"$4}'| sed -e 's/&&&./-/'> XXXX_D.dindel.del cat XXXX_SI.vcf | grep INS | awk '{print $1,"\t",$2,"\t&&&"$5}'| sed -e 's/&&&./+/' > XXXX_SI.dindel.ins cat XXXX_D.dindel.del XXXX_SI.dindel.ins > XXXX.dindel.pindel
cat XXXX_D.vcf XXXX_INV.vcf XXXX_SI.vcf XXXX_TD.vcf | awk '/DEL/ {pos=$2+1; print $1,"\t",pos,"\t-"substr($4,2)}; /RPL|INV/ {pos=$2+1; print $1,"\t",pos,"\t-"substr($4,2)"\n"$1,"\t",pos,"\t+"substr($5,2)}; /INS/ {pos=$2+1; print $1"\t"pos"\t+"substr($5,2)}' > XXXX-all.pindel.dindel
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