Hi all, I have been doing variant calling analysis in human cancer exomes and some variants in the VCF file have genotype like 4/6 or 2/3, is there any explanation for this fact, since I expected to see only 0/1, or 1/1? Thank you very much
is there any explanation for this fact
yes, read the VCF spec: https://samtools.github.io/hts-specs/VCFv4.2.pdf
ALT - alternate base(s): Comma separated list of alternate non-reference alleles. The...
GT : genotype, encoded as allele values separated by either of / or | . The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on.