readout of the output

[nzhun]

Hi,
can you tell me how to read the output file, especially for the *_genotype.tsv? how to filter this file for true positive calls?

thank you,

[mourisl]

The simplest usage is to in the genotype.tsv file as a dataframe, and get the 3rd and 6th columns if the corresponding 5th and 8th column values are greater than 0.

[nzhun]

Thank you for the reply, could you explain what the columns are? On Dec 14, 2023, at 5:01 PM, Li Song ***@***.******@***.***>> wrote: The simplest usage is to in the genotype.tsv file as a dataframe, and get the 3rd and 6th columns if the corresponding 5th and 8th column values are greater than 0. — Reply to this email directly, view it on GitHub<#25 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AENMOQZRMV5JOWMPXSM3BA3YJNZMXAVCNFSM6AAAAABAVQQNG2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJWG42DIMBRGU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[mourisl]

These columns are for "gene_name num_diff_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2 secondary_alleles". You can find more details in the README at https://github.com/mourisl/T1K?tab=readme-ov-file#inputoutput

[nzhun]

Very helpful, thank you On Dec 14, 2023, at 5:53 PM, Li Song ***@***.***> wrote: These columns are for "gene_name num_diff_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2 secondary_alleles". You can find more details in the README at https://github.com/mourisl/T1K?tab=readme-ov-file#inputoutput — Reply to this email directly, view it on GitHub<#25 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AENMOQ4W3UN4F64WHIU342DYJN7OXAVCNFSM6AAAAABAVQQNG2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJWHA3TAMBWGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

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------------------------------------------------- Na Zhu, PhD Associate Research Scientist, Chung Lab, Department of Pediatrics Shen Lab, Department of Systems Biology Columbia University email: ***@***.***