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tgen / phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
MIT License
17 stars 6 forks source link

Sex check #64

Closed ryanrichholt closed 5 years ago

ryanrichholt commented 5 years ago

Add some tool that doesn't require any constitutional genotyping.

PedalheadPHX commented 5 years ago

New approach developed and being implemented by @awchrist, final production ready code templete available in (https://github.com/tgen/toolkit_jkeats/blob/master/pipeline_dev/gender_Check.sh). Running final test were the confidence descriptions have 5 distinct levels (High, Medium-High, Medium, Medium-Low, Low) that reflect different observations.

This uses three approaches to predict gender. The genotype approaches look at overall homozygosity rate and BB alternate genotype rates. They both require 500 tested genotypes for a call, this removes false predictions in MMRF long-inserts. There is also a total read count on Y that is 100% correct on all MMRF patients, which is used as the default prediction and the confidence reflects the level of agreement from the genotyping validation approaches.

PedalheadPHX commented 5 years ago

Summary now available in the jetstream presentation deck

PedalheadPHX commented 5 years ago

Implemented and working