diff --git a/cre.gemini2txt.vcf2db.sh b/cre.gemini2txt.vcf2db.sh index 9d27f25..803b017 100755 --- a/cre.gemini2txt.vcf2db.sh +++ b/cre.gemini2txt.vcf2db.sh @@ -37,6 +37,7 @@ sQuery="select \ qual as Quality,\ gene as Gene,\ clinvar_sig as Clinvar,\ + ensembl_gene_id as Ensembl_gene_id,\ transcript as Ensembl_transcript_id,\ aa_length as AA_position,\ exon as Exon,\ diff --git a/cre.lupus.filter.sh b/cre.lupus.filter.sh new file mode 100755 index 0000000..2a7f955 --- /dev/null +++ b/cre.lupus.filter.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +bname=`basename $1 .csv` + +head -n1 $1 > $bname.lupus.csv +cat $1 | egrep "\"(ACP5|ADAR|C1QA|C1QB|C1QC|C1R|C1S|C2|C3|C4A|C4B|CYBB|DNASE1|DNASE1L3|FASLG|IFIH1|KRAS|MAN2B1|NEIL3|PEPD|PRKCD|PSMA3|PSMB4|PSMB8|PTEN|PTPN11|RAG2|RNASEH2A|RNASEH2B|RNASEH2C|SAMHD1|SHOC2|SLC7A7|TMEM173|TNFRSF6B|TREX1)\"" >> $bname.lupus.csv +#cat $1 | awk -F ',' '$6 ~/^(AP3B1|BLOC1S6|CD27|GATA2|ITK|LYST|NLRC4|PRF1|RAB27A|SH2D1A|SLC7A7|STX11|STXBP2|UNC13D|XIAP)$/{print}' > $bname.lupus.csv diff --git a/cre.lupus.oparina_genes.filter.sh b/cre.lupus.oparina_genes.filter.sh new file mode 100755 index 0000000..f93798b --- /dev/null +++ b/cre.lupus.oparina_genes.filter.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +bname=`basename $1 .csv` + +head -n1 $1 > $bname.lupus.csv +cat $1 | egrep "\"()\"" >> $bname.lupus.oparina.csv +#cat $1 | awk -F ',' '$6 ~/^(AP3B1|BLOC1S6|CD27|GATA2|ITK|LYST|NLRC4|PRF1|RAB27A|SH2D1A|SLC7A7|STX11|STXBP2|UNC13D|XIAP)$/{print}' > $bname.lupus.csv diff --git a/cre.sh b/cre.sh index 7472fcf..17a9b73 100755 --- a/cre.sh +++ b/cre.sh @@ -108,7 +108,7 @@ function f_make_report then export depth_threshold=5 else - export depth_threshold=10 + export depth_threshold=10 fi if [ "$type" == "wes.synonymous" ] || [ "$type" == "wgs" ]