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Export / Query

Export statistics

Export statistics is an special case of export. Instead of export full variants, only the variant cohort statistics are exported.

As for variants export, there are multiple possible output formats:

• VCF : Standard VCF format without samples information, with the stats as values in the INFO column.

  VCF

  ##fileformat=VCFv4.2
  ##FILTER=<ID=.,Description="No FILTER info">
  ##FILTER=<ID=PASS,Description="Valid variant">
  ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes, for each ALT allele, in the same order as listed">
  ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, calculated from AC and AN, in the range (0,1), in the same order as listed">
  ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
  ##INFO=<ID=AFK_AF,Number=A,Type=Float,Description="Allele frequency in the C1 cohort calculated from AC and AN, in the range (0,1), in the same order as listed">
  #CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO
  22    16050115    .    G    A    .    PASS    AC=1;AF=0.001;AN=1000;AFK_AF=0.002008
  22    16050213    .    C    T    .    PASS    AC=1;AF=0.001;AN=1000;AFK_AF=0
  22    16050319    .    C    T    .    PASS    AC=1;AF=0.001;AN=1000;AFK_AF=0
  22    16050607    .    G    A    .    PASS    AC=2;AF=0.002;AN=1000;AFK_AF=0.004016
  
  
  

• TSV (Tab Separated Values). Simple format with each cohort in one column.

  TSV

  #CHR    POS    REF    ALT    ALL_AN    ALL_AC    ALL_AF    ALL_HET    ALL_HOM
  22    16050213    C    T    1000    1    0.001    0.002    0.0
  22    16050607    G    A    1000    2    0.002    0.004    0.0
  22    16050740    A    -    1000    1    0.001    0.002    0.0
  22    16050840    C    G    1000    13    0.013    0.026    0.0
  22    16051075    G    A    1000    2    0.002    0.004    0.0
  22    16051249    T    C    1000    91    0.091    0.162    0.01
  22    16051453    A    C    998    74    0.074    0.144    0.004
  22    16051453    A    G    926    2    0.002    0.144    0.004
  22    16051723    A    -    1000    12    0.012    0.024    0.0
  22    16051816    T    G    1000    2    0.002    0.004    0.0
  

• JSON. Variant model just with minimal information and statistics.

• Population Frequencies (Cellbase mode). Specific JSON format for import into Cellbase variation. It is a Variant model with VariantAnnotation with PupulationFrequencies.

  PopulationFrequencies / Cellbase

  {"names":[],"reference":"T","chromosome":"22","alternate":"C","start":16174643,"annotation":{"populationFrequencies":[{"study":"s1","population":"ALL","refAllele":"T","altAllele":"C","refAlleleFreq":0.999,"altAlleleFreq":0.001,"refHomGenotypeFreq":0.998,"hetGenotypeFreq":0.002,"altHomGenotypeFreq":0.0},{"study":"s1","population":"C1","refAllele":"T","altAllele":"C","refAlleleFreq":0.998,"altAlleleFreq":0.002,"refHomGenotypeFreq":0.996,"hetGenotypeFreq":0.004,"altHomGenotypeFreq":0.0}]},"end":16174643,"type":"SNV","studies":[],"strand":"+","hgvs":{},"length":1}
  {"names":[],"reference":"C","chromosome":"22","alternate":"T","start":16176715,"annotation":{"populationFrequencies":[{"study":"s1","population":"ALL","refAllele":"C","altAllele":"T","refAlleleFreq":0.998,"altAlleleFreq":0.002,"refHomGenotypeFreq":0.996,"hetGenotypeFreq":0.004,"altHomGenotypeFreq":0.0},{"study":"s1","population":"C2","refAllele":"C","altAllele":"T","refAlleleFreq":0.99598396,"altAlleleFreq":0.004016064,"refHomGenotypeFreq":0.99196786,"hetGenotypeFreq":0.008032128,"altHomGenotypeFreq":0.0}]},"end":16176715,"type":"SNV","studies":[],"strand":"+","hgvs":{},"length":1}
  {"names":[],"reference":"C","chromosome":"22","alternate":"A","start":16176724,"annotation":{"populationFrequencies":[{"study":"s1","population":"ALL","refAllele":"C","altAllele":"A","refAlleleFreq":0.999,"altAlleleFreq":0.001,"refHomGenotypeFreq":0.998,"hetGenotypeFreq":0.002,"altHomGenotypeFreq":0.0},{"study":"s1","population":"C2","refAllele":"C","altAllele":"A","refAlleleFreq":0.997992,"altAlleleFreq":0.002008032,"refHomGenotypeFreq":0.99598396,"hetGenotypeFreq":0.004016064,"altHomGenotypeFreq":0.0}]},"end":16176724,"type":"SNV","studies":[],"strand":"+","hgvs":{},"length":1}
  {"names":[],"reference":"T","chromosome":"22","alternate":"C","start":16176769,"annotation":{"populationFrequencies":[{"study":"s1","population":"ALL","refAllele":"T","altAllele":"C","refAlleleFreq":0.999,"altAlleleFreq":0.001,"refHomGenotypeFreq":0.998,"hetGenotypeFreq":0.002,"altHomGenotypeFreq":0.0},{"study":"s1","population":"C2","refAllele":"T","altAllele":"C","refAlleleFreq":0.997992,"altAlleleFreq":0.002008032,"refHomGenotypeFreq":0.99598396,"hetGenotypeFreq":0.004016064,"altHomGenotypeFreq":0.0}]},"end":16176769,"type":"SNV","studies":[],"strand":"+","hgvs":{},"length":1}
  {"names":[],"reference":"T","chromosome":"22","alternate":"A","start":16176926,"annotation":{"populationFrequencies":[{"study":"s1","population":"C3","refAllele":"T","altAllele":"A","refAlleleFreq":0.5,"altAlleleFreq":0.5,"refHomGenotypeFreq":0.0,"hetGenotypeFreq":1.0,"altHomGenotypeFreq":0.0},{"study":"s1","population":"ALL","refAllele":"T","altAllele":"A","refAlleleFreq":0.473,"altAlleleFreq":0.527,"refHomGenotypeFreq":0.166,"hetGenotypeFreq":0.614,"altHomGenotypeFreq":0.22},{"study":"s1","population":"C1","refAllele":"T","altAllele":"A","refAlleleFreq":0.474,"altAlleleFreq":0.526,"refHomGenotypeFreq":0.164,"hetGenotypeFreq":0.62,"altHomGenotypeFreq":0.216},{"study":"s1","population":"C2","refAllele":"T","altAllele":"A","refAlleleFreq":0.4698795,"altAlleleFreq":0.5301205,"refHomGenotypeFreq":0.16465864,"hetGenotypeFreq":0.6104418,"altHomGenotypeFreq":0.2248996}]},"end":16176926,"type":"SNV","studies":[],"strand":"+","hgvs":{},"length":1}
  
  
  

Import