User:Lindenb/Notebook/UMR915/2012/02/22

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VARKIT=${HOME}/src/variationtoolkit/bin
gunzip -c predictions.txt.gz | grep -v "SnpEff" | awk -F'	' '(!($$16=="INTERGENIC" || $$16=="UPSTREAM" || $$16=="DOWNSTREAM"|| $$16=="INTRON" || $16=="UTR_3_PRIME" ||  $16=="UTR_5_PRIME"))' |\
awk '{printf("%s_%s_%s_%s\t%s\n",$1,$2,$3,$4,$0);}'| sort -t '	' -k1,1 > _jeter1.txt


gunzip -c all.vcf.gz |\
${VARKIT}/vcf2snpeff |\
awk '{printf("%s_%s_%s_%s\t%s\n",$1,$2,$3,$4,$0);}'| cut -f 1,6-| sort -t '	' -k1,1 > _jeter2.txt