From 92be9c15577233a56e048830e9a767585d1e5724 Mon Sep 17 00:00:00 2001 From: Yi Li Date: Thu, 3 Apr 2014 21:43:27 -0700 Subject: [PATCH] Update README.md --WES added --- README.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 2c6a716..c1785cc 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -README for PyLOH 1.1.3 +README for PyLOH 1.2.0 ====================== @@ -23,7 +23,8 @@ heterozygosity - within an unified probabilistic framework. We derive algorithms to solve our model, and implement them in a software package called PyLOH. We also introduce a novel visualization method "BAF heat map" to to characterize -the cluster pattern of LOH. +the cluster pattern of LOH. If you have any questions, please +email yil8@uci.edu INSTALL @@ -113,6 +114,9 @@ be done by running **--segments_bed** Use the genome segmentation stored in SEGMENTS.bed. If not provided, use 22 autosomes as the segmentaion. But using automatic segmentation algorithm to generate SEGMENTS.bed is highly recommended, such as [BICseq](http://compbio.med.harvard.edu/Supplements/PNAS11.html). +**--WES** Flag indicating whether the BAM files are whole exome sequencing(WES) or not. If not provided, the BAM files +are assumed to be whole genome sequencing(WGS). + **--min_depth** Minimum depth in both normal and tumor sample required to use a site in the analysis. **--min_base_qual** Minimum base quality required for each base. @@ -182,7 +186,6 @@ column in a *.PyLOH.segments file is listed here: | Column | Definition | | :--------------- | :-------------------------------------| -| allele_type | Estimated allele type of the segment | | copy_number | Estimated copy number of the segment | **\*.PyLOH.purity** Estimated tumor purity. @@ -212,3 +215,8 @@ $ BICseq2bed.py segments.BICseq segments.bed --seg_length 1000000 ``` **--seg_length** Only convert segments with length longer than the threshold. + + +Reference +========= +Li, Y., Xie, X. (2014). Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. Bioinformatics.