diff --git a/vcfanno/crg.vcfanno_hg38.conf b/vcfanno/crg.vcfanno_hg38.conf index cbd95a4..dd0314a 100644 --- a/vcfanno/crg.vcfanno_hg38.conf +++ b/vcfanno/crg.vcfanno_hg38.conf @@ -1,52 +1,9 @@ -#gnomad v.2.1.1 exomes (lifted over) +#gnomad v.4.1.0 merged joint frequency (hg38) [[annotation]] -file="gnomad_exome.2.1.1_LIFTOVER.vcf.gz" -fields=["AC","nhomalt","AF_popmax","AN","AC_male"] -names=["gnomad_ac_es","gnomad_hom_es","gnomad_af_es","gnomad_an_es","gnomad_male_ac_es"] -ops=["self","self","self","self","self"] - -#gnomad v.3.1.2 genomes (native hg38) -[[annotation]] -file="gnomad_genomes_v.3.1.2.vcf.gz" -fields=["AC", "nhomalt","AF_popmax","AN","AC_XY"] -names=["gnomad_ac_gs", "gnomad_hom_gs","gnomad_af_gs","gnomad_an_gs","gnomad_male_ac_gs"] -ops=["self","self","self","self","self"] - -[[postannotation]] -fields=["gnomad_ac_es","gnomad_ac_gs"] -op="sum" -name="gnomad_ac" -type="Integer" - -[[postannotation]] -fields=["gnomad_hom_es","gnomad_hom_gs"] -op="sum" -name="gnomad_hom" -type="Integer" - -[[postannotation]] -fields=["gnomad_af_es","gnomad_af_gs"] -op="max" -name="gnomad_af_popmax" -type="Float" - -[[postannotation]] -fields=["gnomad_an_es","gnomad_an_gs"] -op="sum" -name="gnomad_an" -type="Integer" - -[[postannotation]] -fields=["gnomad_ac","gnomad_an"] -op="div2" -name="gnomad_af" -type="Float" - -[[postannotation]] -fields=["gnomad_male_ac_es","gnomad_male_ac_gs"] -op="sum" -name="gnomad_male_ac" -type="Integer" +file="gnomad_merged_joint_frequencies_v4.1.0.vcf.gz" +fields=["AC_joint", "nhomalt_joint","AF_joint","AF_grpmax_joint","AN_joint","AC_joint_XY","fafmax_faf95_max_joint","FILTER"] +names=["gnomad_ac", "gnomad_hom","gnomad_af","gnomad_af_grpmax","gnomad_an","gnomad_male_ac","gnomad_fafmax_faf95_max","gnomad_filter"] +ops=["self","self","self","self","self","self","self","self"] [[annotation]] file="dbsnp-151.vcf.gz"