Changes

  --referencegenome ''referencegenome file''

  --referencegenome ''referencegenome file''

  --dbSNPfile      ''optional'' ''dbsnp position file, will provide more accurate background mismatch rate if excluding dbSNP positions''

  --dbSNPfile      ''optional'' ''two-column'' ''dbsnp position file, will provide more accurate background mismatch rate if excluding dbSNP positions (e.g. 5 123456)''

  --lanefile        ''a list of lane file with path''

  --lanefile        ''a list of lane file with path''

  --pedfile        ''genotype information of the samples for checking ''

  --pedfile        ''genotype information of the samples for checking ''

  --datfile        ''a companion data file for pedigree file (each row: M snpname, e.g. M rs1234)''

  --datfile        ''a companion data file for pedigree file (each row: M snpname, e.g. M rs1234)''

  --mapfile        ''a companion data file for pedigree file (each row: chr snpname pos, e.g. 5 rs1234 56789)''

  --mapfile        ''a companion data file for pedigree file (each row: chr snpname pos, e.g. 5 rs1234 56789)''

=== Basic Output Options ===

=== Basic Output Options ===