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Old 12-11-2012, 06:52 AM   #1
Location: Pavia

Join Date: Nov 2011
Posts: 25
Default VarScan2 somatic output (genotype call)

Hi everyone,
I'm using varscan2 to call somatic variants.
I have some problem to undestand some field of the output, in particular I don't understand what kind of codify they use both for genotype call for Normal sample and tumor sample.

here some row of the output:

PHP Code:
chrom    position    ref    var    normal_reads1    normal_reads2    normal_var_freq    normal_gt    tumor_reads1    tumor_reads2    tumor_var_freq    tumor_gt    somatic_status    variant_p_value    somatic_p_value    tumor_reads1_plus    tumor_reads1_minus    tumor_reads2_plus    tumor_reads2_minus

chr1    69897    T    C    393    214    35
,26%    Y    570    285    33,33%    Y    Germline    2.393941203174513E-173    0.793896726900893    244    326    128    157    165    228    106    108
chr1    131552    G    T    18    6    25
%    K    20    3    13,04%    K    Germline    0.0012810738523452987    0.922366186932137    15    5    2    1    16    2    6    0 
what does it mean a genotype call like K or Y?
thanks in advance for your help
desmo is offline   Reply With Quote
Old 12-27-2012, 08:49 AM   #2
Location: St. Louis

Join Date: Mar 2009
Posts: 62


Those are heterozygous genotypes represented as IUPAC ambiguity codes.
dkoboldt is offline   Reply With Quote

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