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removing more gnomad fields in annotation_strip
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naumenko-sa committed Oct 28, 2019
1 parent feae01b commit 859a134
Showing 1 changed file with 11 additions and 1 deletion.
12 changes: 11 additions & 1 deletion cre.annotation.strip.sh
Original file line number Diff line number Diff line change
@@ -1,6 +1,16 @@
#!/bin/bash

bname=`basename $1 .vcf.gz`
vt rminfo -t CSQ,ANN,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,vcfanno_gnomad_ac_es,vcfanno_gnomad_hom_es,vcfanno_gnomad_af_es,vcfanno_gnomad_an_es,vcfanno_gnomad_ac_gs,vcfanno_gnomad_hom_gs,vcfanno_gnomad_af_gs,vcfanno_gnomad_an_gs,vcfanno_gnomad_ac,vcfanno_gnomad_af_popmax,vcfanno_gnomad_an,vcfanno_gnomad_af \
vt rminfo -t CSQ,ANN,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,vcfanno_gnomad_ac_es,vcfanno_gnomad_hom_es,vcfanno_gnomad_af_es,\
vcfanno_gnomad_an_es,vcfanno_gnomad_ac_gs,vcfanno_gnomad_hom_gs,vcfanno_gnomad_af_gs,vcfanno_gnomad_an_gs,vcfanno_gnomad_ac,\
vcfanno_gnomad_af_popmax,vcfanno_gnomad_an,vcfanno_gnomad_af,gnomad_gc,gnomad_gc_female,gnomad_gc_male
$1 -o $bname.no_anno.vcf.gz
tabix $bname.no_anno.vcf.gz

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