v1.0.17

• QUAL, AB, GQ, DP, FILTER are available in custom Info List
• New maxCohortGT argument, in cohort mode, integer to set to maximum of individuals sharing the same genotype (default = 1)
• New gnomAD_nhomalt argument , path to file containing gnomAD number of homozygous, added to gnomAD comment

v1.0.16

• Fix inheritance (exclude chrX)

v1.0.15

• FILTER is back
• Fix inheritance (logRatio range + exclude chrX)
• genome build in URL

v1.0.13

• Merge CHROM-POS-REF-ALT columns
• Send Func.refGene and ID columns into MPA_impact comments
• URL to create variant in Mobidetails in MPA_impact column
• OMIM (genemap2) annotation rescue for multiple genes variant (to compensate for annovar bad annotation)
• Fix inheritance computation : range -0.13 to 0.1, and adjust with pooled parents

v1.0.11

• Add CANDIDATES TAG to a new column in poor coverage file

v1.0.10

• Add gnomAD_exome_SAS annotation in gnomAD_exome comment
• Apply skipCaseWT option in duo context (case and dad defined OR case and mum defined) to skip 0/0 case genotype
• Remove duplicated gene names

v1.0.9

• Fix inheritance computing with skipCaseWT option

• Update ACMG incidental finding gene list according to v3.2, adding CALM1, CALM2, CALM3 genes (https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/)

v1.0.8

• gnomAD columns names are frozen to gnomAD_Genome and gnomAD_Exome

• Update ACMG incidental finding gene list according to v3.1 (https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/)

v1.0.7

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

v1.0.6

• Extends intersectVCF: add INFO field if any differences for OMIM, CLNSIG and MPA_impact
• In trio context, case, dad, mum is removed from affected list
• Annotate Poorcoverage as well with candidates genes if provided