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@thomasguignard thomasguignard released this 31 Jan 15:34
· 22 commits to master since this release
v1.0.7
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Add 2 new arguments to modify gnomAD format:
--gnomadGenome <comma separated list of gnomad genome annotation fields that will be displayed as gnomAD comments. First field of the list will be filtered regarding to popFreqThr argument, and it will be considered as column name. (default fields are hard-coded gnomAD_genome_ALL like) >
--gnomadExome <comma separated list of gnomad exome annotation fields that will be displayed as gnomAD comments. First field of the list will be treated as column name. (default fields are hard-coded gnomAD_exome_ALL like) >

Since it gives column name, first field must be different between exome and genome.

examples:
--gnomadExome AF,AF_popmax,AF_male,AF_female,AF_raw,AF_afr,AF_sas,AF_amr,AF_eas,AF_nfe,AF_fin,AF_asj,AF_oth,non_topmed_AF_popmax,non_neuro_AF_popmax,non_cancer_AF_popmax,controls_AF_popmax
--gnomadGenome gnomAD_genome_ALL,gnomAD_genome_AFR,gnomAD_genome_AMR,gnomAD_genome_ASJ,gnomAD_genome_EAS,gnomAD_genome_FIN,gnomAD_genome_NFE,gnomAD_genome_OTH
or
--gnomadGenome gnomad312_AF,gnomad312_AF_raw,gnomad312_AF_XX,gnomad312_AF_XY,gnomad312_AF_popmax,gnomad312_AF_faf95_popmax,gnomad312_AF_afr,gnomad312_AF_ami,gnomad312_AF_amr,gnomad312_AF_asj,gnomad312_AF_eas,gnomad312_AF_fin,gnomad312_AF_mid,gnomad312_AF_nfe,gnomad312_AF_oth,gnomad312_AF_sas

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