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Kurt-Hetrick / CFTR_Full_Gene_Sequencing_Pipeline

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gender identification #8

Closed Kurt-Hetrick closed 3 years ago

Kurt-Hetrick commented 4 years ago

from barcode snps, can this be automated (or is there a desire to have this done automatically given the barcode snps).

Kurt-Hetrick commented 3 years ago

the number of heterozygous chrX SNPs and the number of high quality (Pass + qual>100) chr Y SNPs for each sample.

Male= no heterozygous chrX SNPs + 6 high quality chrY SNPs Female= at least 1 heterozygous chrX SNP + 0 high quality chrY SNPs (It's very rare, but occasionally we get a female without any heterozygous chrX SNPs. As long as they don't have any high quality chrY calls we say that the sex is consistent)

exclude the 1 X PAR snp.

Kurt-Hetrick commented 3 years ago

done, since there are only 5 y snps present, 5 is the cut-off for male determination. if criteria for male or female is not met, sex is undetermined.