Read sequence is called targetSequences in the output. While in the mutation format description in docs we have
"
Mutations are encoded as a list of single-nucleotide edits (similar to what is used in definition of Levenshtein distance, i.e. insertions, deletions or substitutions); if one apply these mutations to aligned subsequence of target sequence, one will obtain aligned subsequence of query sequence.
"
so here the target is actually the germline sequence and query is the read sequence. Consider renaming targetSequences -> querySequences in the output table?
dbolotin
commented
5 years ago
Read sequence is called
targetSequencesin the output. While in the mutation format description in docs we have" Mutations are encoded as a list of single-nucleotide edits (similar to what is used in definition of Levenshtein distance, i.e. insertions, deletions or substitutions); if one apply these mutations to aligned subsequence of target sequence, one will obtain aligned subsequence of query sequence. "
so here the
targetis actually the germline sequence andqueryis the read sequence. Consider renamingtargetSequences -> querySequencesin the output table?