Added methods for sex determination tool

content/03.methods.md

@@ -87,3 +87,13 @@ We annotated putative driver fusions and prioritized fusions lists with kinases,
 We also added chimerDB [@doi:10.1093/nar/gkw1083] annotations to both driver and prioritized fusion list.
 
 ### Clinical Data Harmonization
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+#### Sex Determination
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+We wrote a sex determination tool for sequenced DNA samples to determine concordance to reported gender and identify contaminated samples.
+We set up a tool using CWL on Cavatica to identify sex based on read coverage on Chromosome X and Chromosome Y.
+We used the idxstats utility from SAMTOOLS [@pmid:19505943] to generate read lengths, the number of mapped reads, and the corresponding chromosomal location.
+We calculated the normalized read counts for the X and Y chromosome using the generated statistics and the fraction of total normalized X and Y chromosome reads that were on the Y chromosome.
+We determined that if this fraction was less than 0.2, the sample's germline sex prediction was Female by reviewing the fractions for samples whose had reported genders.
+If this fraction was between 0.4 and 0.6, the sample's germline sex prediction was Male.
+Any remaining uncategorized fraction was marked Unknown.