Merge pull request #40 from shrivatsk/patch-2

Added methods for sex determination tool

content/03.methods.md

@@ -117,3 +117,16 @@ 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
+
+#### Prediction of participants' genetic sex
+
+The clinical metadata provided included a reported gender.
+We used DNA data, in concert with the reported gender, to predict participant genetic sex so that we could identify sexually dimorphic outcomes.
+This analysis could also reveal samples that may have been contaminated in certain circumstances.
+We used the idxstats utility from SAMTOOLS [@pmid:19505943] to calculate read lengths, the number of mapped reads, and the corresponding chromosomal location for reads to the X and Y chromosomes.
+We used the fraction of total normalized X and Y chromosome reads that were attributed to the Y chromosome as a summary statistic.
+We reviewed this statistic in the context of reported gender and determined that a threshold of less than 0.2 clearly delineated female samples.
+Fractions greater than 0.4 were predicted to be males.
+Samples with values in the range [0.2, 0.4] were marked as unknown.
+We ran this analysis through [CWL](https://github.com/d3b-center/sex-determination-tool) on Cavatica.
+Resulting calls were added to the clinical metadata as `germline_sex_estimate`.