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CCF-CAYA IVA Varaint Prioritisation Filter parametes

  • Export Date: 2019-Feb-05 06:40:19
  • Analysis Name : CCF-CAYA-012519

Software versions

Ingenuity Variant Analysis version 5.4.20190121 Content versions: 
  CADD (v1.3), 
  Allele Frequency Community (2018-09-06), 
  EVS (ESP6500SI-V2), 
  Refseq Gene Model (2018-07-10), 
  JASPAR (2013-11), 
  Ingenuity Knowledge Base Snapshot Timestamp (2019-01-06 00:23:50.0), 
  Vista Enhancer (2012-07), 
  Clinical Trials (Stepford 190106.000), 
  PolyPhen-2 (v2.2.2), 
  1000 Genome Frequency (phase3v5b), 
  ExAC (0.3.1), 
  iva (Oct 4 11:04 iva-1.0.736.jar), 
  PhyloP (2009-11), 
  DbSNP (151), 
  TargetScan (6.2), 
  GENCODE (Release 28), 
  CentoMD (5.0), 
  Ingenuity Knowledge Base (Stepford 190106.000), 
  OMIM (May 26, 2017), 
  gnomAD (2.0.1), 
  BSIFT (2016-02-23), 
  TCGA (2013-09-05), 
  Clinvar (2018-08-01), 
  DGV (2016-05-15), 
  COSMIC (v86),
  HGMD (2018.3), 
  SIFT4G (2016-02-23)

Filter Description:

  • Starting with 55,346 variants spanning 18,630 genes, variants were:

  • kept with call quality at least 20.0 in cases or at least 20.0 in controls AND pass upstream pipeline filtering AND with read depth at least 20.0 in cases or at least 20.0 in controls AND with allele fraction at least 20.0 in cases or at least 20.0 in controls with genotype quality at least 30.0 in cases or at least 30.0 in controls AND outside top 5.0% most exonically variable 100base windows in healthy public genomes (1000 genomes)

  • excluded that are observed with an allele frequency greater than or equal to 1.0% of the genomes in the 1000 genomes project OR greater than or equal to 1.0% of the NHLBI ESP exomes (All) OR greater than or equal to 1.0% of the ExAC Frequency OR greater than or equal to 1.0% of the gnomAD Maximum Frequency OR Filter variants unless established Pathogenic common variant

  • kept (up to 20 bases into intron) that are experimentally observed to be associated with a phenotype: Pathogenic, Possibly Pathogenic

  • excluded that are on chromosome MT

  • kept which occur in at least 1 of the case samples at the variant level in the Case samples AND not which occur in at least 1 of the control samples at the variant level in the Control Samples

  • kept (up to 20 bases into intron) that are experimentally observed to be associated with a phenotype: Pathogenic, Possibly Pathogenic OR Disease-associated according to HGMD OR predicted to disrupt splicing by MaxEntScan

Sample Table:

BarCode	Name	Description	Subject	Status
CCF13084-01-001	CCF13084-01-001	CCF13084-01-001		CASE
CCF13090-01-001	CCF13090-01-001	CCF13090-01-001		CASE
CCF13037-01-001	CCF13037-01-001	CCF13037-01-001		CASE
CCF13105-01-001	CCF13105-01-001	CCF13105-01-001		CASE
CCF10699-01-001_R1	CCF10699-01-001_R1	CCF10699-01-001_R1		CASE
CCF10723_TAAGGCG-TAAGGA_R1.fastq	CCF10723_TAAGGCG-TAAGGA_R1.fastq	CCF10723_TAAGGCG-TAAGGA_R1.fastq		CASE
CCF10769_CGTACTA-TAAGGA_R1.fastq	CCF10769_CGTACTA-TAAGGA_R1.fastq	CCF10769_CGTACTA-TAAGGA_R1.fastq		CASE
CCF10770_AGGCAGA-TAAGGA_R1.fastq	CCF10770_AGGCAGA-TAAGGA_R1.fastq	CCF10770_AGGCAGA-TAAGGA_R1.fastq		CASE
CCF10771_TCCTGAG-TAAGGA_R1.fastq	CCF10771_TCCTGAG-TAAGGA_R1.fastq	CCF10771_TCCTGAG-TAAGGA_R1.fastq		CASE
CCF10781_GGACTCC-TAAGGA_R1.fastq	CCF10781_GGACTCC-TAAGGA_R1.fastq	CCF10781_GGACTCC-TAAGGA_R1.fastq		CASE
CCF10782_TAGGCAT-TAAGGA_R1.fastq	CCF10782_TAGGCAT-TAAGGA_R1.fastq	CCF10782_TAGGCAT-TAAGGA_R1.fastq		CASE
CCF10783_CTCTCTA-TAAGGA_R1.fastq	CCF10783_CTCTCTA-TAAGGA_R1.fastq	CCF10783_CTCTCTA-TAAGGA_R1.fastq		CASE
CCF10839_GCTACGC-TAAGGA_R1.fastq	CCF10839_GCTACGC-TAAGGA_R1.fastq	CCF10839_GCTACGC-TAAGGA_R1.fastq		CASE
CCF10903_AAGAGGC-TAAGGA_R1.fastq	CCF10903_AAGAGGC-TAAGGA_R1.fastq	CCF10903_AAGAGGC-TAAGGA_R1.fastq		CASE
CCF11008_GTAGAGG-TAAGGA_R1.fastq	CCF11008_GTAGAGG-TAAGGA_R1.fastq	CCF11008_GTAGAGG-TAAGGA_R1.fastq		CASE
CCF11143_TAAGGCG-CTGCAT_R1.fastq	CCF11143_TAAGGCG-CTGCAT_R1.fastq	CCF11143_TAAGGCG-CTGCAT_R1.fastq		CASE
CCF11170_CGTACTA-CTGCAT_R1.fastq	CCF11170_CGTACTA-CTGCAT_R1.fastq	CCF11170_CGTACTA-CTGCAT_R1.fastq		CASE
CCF11171_AGGCAGA-CTGCAT_R1.fastq	CCF11171_AGGCAGA-CTGCAT_R1.fastq	CCF11171_AGGCAGA-CTGCAT_R1.fastq		CASE
CCF11485_GGACTCC-CTGCAT_R1.fastq	CCF11485_GGACTCC-CTGCAT_R1.fastq	CCF11485_GGACTCC-CTGCAT_R1.fastq		CASE
CCF11521-01-001_R1	CCF11521-01-001_R1	CCF11521-01-001_R1		CASE
CCF11769	CCF11769	CCF11769		CASE
CCF11777-01-001_R1	CCF11777-01-001_R1	CCF11777-01-001_R1		CASE
CCF11805-01-001_R1	CCF11805-01-001_R1	CCF11805-01-001_R1		CASE
CCF11813-01-001_R1	CCF11813-01-001_R1	CCF11813-01-001_R1		CASE
CCF11814	CCF11814	CCF11814		CASE
CCF11829-01-001_R1	CCF11829-01-001_R1	CCF11829-01-001_R1		CASE
CCF11834	CCF11834	CCF11834		CASE
CCF11835	CCF11835	CCF11835		CASE
CCF11848	CCF11848	CCF11848		CASE
CCF11884	CCF11884	CCF11884		CASE
CCF11930	CCF11930	CCF11930		CASE
CCF11946	CCF11946	CCF11946		CASE
CCF11950	CCF11950	CCF11950		CASE
CCF11987	CCF11987	CCF11987		CASE
CCF11993	CCF11993	CCF11993		CASE
CCF12007-01-001_R1	CCF12007-01-001_R1	CCF12007-01-001_R1		CASE
CCF12020	CCF12020	CCF12020		CASE
CCF12039	CCF12039	CCF12039		CASE
CCF12040-01-001_R1	CCF12040-01-001_R1	CCF12040-01-001_R1		CASE
CCF12064-01-001_R1	CCF12064-01-001_R1	CCF12064-01-001_R1		CASE
CCF12081	CCF12081	CCF12081		CASE
CCF12082-01-001_R1	CCF12082-01-001_R1	CCF12082-01-001_R1		CASE
CCF12094	CCF12094	CCF12094		CASE
CCF12130	CCF12130	CCF12130		CASE
CCF12189	CCF12189	CCF12189		CASE
CCF12237-01-001_S1_R1	CCF12237-01-001_S1_R1	CCF12237-01-001_S1_R1		CASE
CCF12311-01-001_S2_R1	CCF12311-01-001_S2_R1	CCF12311-01-001_S2_R1		CASE
CCF12327-01-001_S3_R1	CCF12327-01-001_S3_R1	CCF12327-01-001_S3_R1		CASE
CCF11804-01-001	CCF11804-01-001	CCF11804-01-001		CASE
CCF13072-01-001	CCF13072-01-001	CCF13072-01-001		CASE
5476M	5476M	5476M		CONTROL
6472M	6472M	6472M		CONTROL
4506M	4506M	4506M		CONTROL
4469M	4469M	4469M		CONTROL
4367M	4367M	4367M		CONTROL
4310M	4310M	4310M		CONTROL
4214M	4214M	4214M		CONTROL
4206M	4206M	4206M		CONTROL
3298M	3298M	3298M		CONTROL
3048M	3048M	3048M		CONTROL
3083M	3083M	3083M		CONTROL
1478M	1478M	1478M		CONTROL
2994M	2994M	2994M		CONTROL