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:
what does it mean a genotype call like K or Y?
thanks in advance for your help
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
thanks in advance for your help
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