From: Fully automated pipeline for detection of sex linked genes using RNA-Seq data
Mother must be homozygous (X 1 X 1 ). | Especially is checked whether mother contains any father variants (X2). Limited tolerance of these variants is described in Table 3. |
Sons must be same as mother (X 1 ). | First, we have to exclude male variants (variants shared between father and son but absent in daughter). Then, sons must contain only X1 variants of mother. |
Father must differ from mother. | Father must have at least one SNP (X2) in which it differs from mother. |
Daughters must have mother and father alleles (X 1 X 2 ). | Only heterozygous daughter contigs are taken into account. These daughter variants must be subset of father variants. |
Daughters and sons cannot have any intersection. | Sons are tested if they contain daughter variants with tolerance described in Table 3. Similarly, daughters are tested for presence of son variants. |
Sufficient coverage. | Average depth per nucleotide must be at least 0.75 (=in contig of length 100, there must be at least 75 nucleotides present/mapped). |