Handling of sex chromosomes

When using the SeqMan NGen wizard, certain workflows allow you to specify the subject’s Gender in the Assembly Options screen.

*Note for command-line users: When using the command-line version of XNG, the sex of the subject is instead specified using the assembleTemplate command by setting the query parameter value to male, female, or unknown.

SeqMan NGen treats all non-template package chromosomes as diploid, unless otherwise specified. However, SeqMan NGen’s XNG assembler does recognize sex chromosomes in DNASTAR genome template packages. Since some regions of the X and Y chromosomes are homologous, read placement may be more accurate in females when reads are not falsely assigned to the Y.

Special handling of sex chromosomes occurs in two circumstances:

During the placement/layout of reads:

All samples in an assembly must be of the same sex; different sexes cannot be specified for individual MID samples. Chromosomes are recognized by the genome template package short name (X Y W Z). One of the names must match exactly. Humans and many other animals have X/Y, while the chicken (Gallus gallus) has a W/Z. For some genome template packages, such as the cow (Bos taurus), Y exists biologically, but has not been sequenced and is not provided in the genome template package.

Sex influences read placement as follows:

• If sex is left Unknown, all chromosomes will be available.

• If sex is set to Female, no reads are placed against the Y chromosome.

• If sex is set to Male, the haploid variant caller is used for both X and Y chromosomes; no reads are placed against the W chromosome.

+When calling SNPs and using the Bayesian SNP caller: +

Bayesian SNP calling is also modified by taking the sex chromosome into account. The XNG script normally controls whether calling is done as diploid or haploid. Whenever haploid is specified as a SNP method all templates are haploid. However even when diploid is chosen:

• chromosomes Y or Z are always haploid

• chromosome X is haploid for males, diploid for female or unknown

• chromosome W is haploid for females, diploid for male or unknown

The mitochondrion is considered diploid, though it would usually be polyploid. If mitochondria are of interest, a separate assembly should be done using the simple SNP method, since the Bayesian caller depends on knowing that there are one or two chromosomes.

Special handling of sex chromosomes can be disabled in an XNG script by setting noSexChromosomes:true. Changing the short name of a chromosome in a genome template package will cause it to revert to normal autosomal behavior in all scripts using that package.