From 8532637adb12d2d61db8393af77b39c8677638e5 Mon Sep 17 00:00:00 2001 From: Li Date: Fri, 29 Sep 2023 11:15:20 -0400 Subject: [PATCH] Update readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e1b327d..1a07143 100644 --- a/README.md +++ b/README.md @@ -91,9 +91,9 @@ The alternative input to T1K is the alignment BAM file (-b), which requires -f a T1K outputs several files. t1k_genotype.tsv is the main output file holding the genotyping result, where the allele for each gene is on its own line with format: - gene_name num_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2 + gene_name num_diff_alleles allele_1 abundance_1 quality_1 allele_2 abundance_2 quality_2 -In the case of missing allele, the triple (allele, abundance, quality) will be ". 0 -1". **We recommend to ignore alleles with quality less or equal to 0**. +In the case of missing alleles or homozygous alleles, the triple (allele, abundance, quality) will be ". 0 -1" as place holders. **We recommend to ignore alleles with quality less or equal to 0**. The other outputs files are: