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gnomad V4 update #231

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gnomad V4 update #231

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fc28bfe
Update gnomad V4 annotation source
anjalijain22 Aug 13, 2024
78cc88d
Add gnomad_filter column
anjalijain22 Sep 17, 2024
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53 changes: 5 additions & 48 deletions vcfanno/crg.vcfanno_hg38.conf
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Original file line number Diff line number Diff line change
@@ -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"
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