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Index


Annotate


Custom annotation

Calculate Statistics

Define cohorts

Remove


Import


Export

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">
    #CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO
    22    16050115    .    G    A    .    PASS    AC=1;AF=0.001;AN=1000
    22    16050213    .    C    T    .    PASS    AC=1;AF=0.001;AN=1000
    22    16050319    .    C    T    .    PASS    AC=1;AF=0.001;AN=1000
    22    16050607    .    G    A    .    PASS    AC=2;AF=0.002;AN=1000
    
    
    
  • 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
    
  • cellbase
  • json



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