cre.annotation.strip.sh

#!/bin/bash

bname=`basename $1 .vcf.gz`
vt rminfo -t CSQ,af_adj_exac_afr,af_adj_exac_amr,af_adj_exac_eas,af_adj_exac_fin,af_adj_exac_nfe,af_adj_exac_oth,af_adj_exac_sas,af_exac_all,ac_exac_all,an_exac_all,ac_adj_exac_afr,an_adj_exac_afr,ac_adj_exac_amr,an_adj_exac_amr,ac_adj_exac_eas,an_adj_exac_eas,ac_adj_exac_fin,an_adj_exac_fin,ac_adj_exac_nfe,an_adj_exac_nfe,ac_adj_exac_oth,an_adj_exac_oth,ac_adj_exac_sas,an_adj_exac_sas,common_pathogenic,max_aaf_all,num_exac_Het,num_exac_Hom,rs_ids,af_1kg_amr,af_1kg_eas,af_1kg_sas,af_1kg_afr,af_1kg_eur,af_1kg_all,fitcons,encode_consensus_gm12878,encode_consensus_h1hesc,encode_consensus_helas3,encode_consensus_hepg2,encode_consensus_huvec,encode_consensus_k562,dgv,hapmap1,hapmap2,gnomAD_AF,gnomAD_AFR_AF,gnomAD_AMR_AF,gnomAD_ASJ_AF,gnomAD_EAS_AF,gnomAD_FIN_AF,gnomAD_NFE_AF,gnomAD_OTH_AF,gnomad_ac_es,gnomad_hom_es,gnomad_af_es,gnomad_an_es,gnomad_ac_gs,gnomad_hom_gs,gnomad_af_gs,gnomad_an_gs,gnomad_ac,gnomad_af_popmax,gnomad_an,gnomad_af,clinvar_pathogenic,clinvar_sig,CADD_phred,phyloP20way_mammalian,phastCons20way_mammalian,Vest3_score,Revel_score,Gerp_score \
	     $1 -o $bname.no_anno.vcf.gz
tabix $bname.no_anno.vcf.gz