HLA and LOH-HLA data - Githubissues

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HLA and LOH-HLA data #1412

Open dippindots opened 3 years ago

dippindots commented 3 years ago

Prepare HLA and LOH-HLA data for 40k study:

LOH-HLA data: make script to generate LOH-HLA data

For patients with multiple normals, keep the one has TRUE in use_for_patient_level_genotype column.
Columns needed (prefix with A1 A2 B1 B2 C1 C2 A B C will be created by merging 3 rows into one by HLA_gene column)

patient	num_distinct_hla_alleles	A1_HLA_A_type	A2_HLA_A_type	B1_HLA_A_type	B2_HLA_A_type	C1_HLA_A_type	C2_HLA_A_type	A1_HLA_type1copyNum_withBAFBin	A2_HLA_type2copyNum_withBAFBin	B1_HLA_type1copyNum_withBAFBin	B2_HLA_type2copyNum_withBAFBin	C1_HLA_type1copyNum_withBAFBin	C2_HLA_type2copyNum_withBAFBin	PVal_unique	A_LossAllele	B_LossAllele	C_LossAllele	numMisMatchSitesCov	propSupportiveSites

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