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yil8 committed Sep 30, 2013
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Expand Up @@ -73,13 +73,13 @@ USAGE
Overview
--------
PyLOH is composed of three modules:
* `preprocess`. Preprocess the reads aliments of paired normal-tumor samples in BAM format and produces the paired counts file,
* `preprocess`. Preprocess the reads aliments of paired normal-tumor samples in BAM format and produce the paired counts file,
preprocessed segments file and preprocessed BAF heat map file as output.

* `run_model`. Take the paired counts file and preprocessed segments file as input, estimates tumor purity, the copy number and the
* `run_model`. Take the paired counts file and preprocessed segments file as input, estimate tumor purity, the copy number and the
allele type of each segment.

* `postprocess`. Take the preprocessed BAF heat map file as input and plots the BAF heat map for each segment as output.
* `postprocess`. Take the preprocessed BAF heat map file as input and plot the BAF heat map for each segment as output.

The general workflow of PyLOH is this
![alt tag](https://github.com/uci-cbcl/PyLOH/blob/gh-pages/images/workflow.png?raw=true)
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**BASENAME** The base name of preprocessed files to be created.

**--segments_bed SEGMENTS.bed** Use the genome segmentation stored in SEGMENTS.bed. If not provided, use 22 autosomes as the segmentaion.
But using automatic segmentation algorithm is highly recommended, such as [BICseq](http://compbio.med.harvard.edu/Supplements/PNAS11.html).
**--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).

**--min_depth** Minimum depth in both normal and tumor sample required to use a site in the analysis.

Expand All @@ -129,8 +129,8 @@ $ PyLOH.py run_model BASENAME --allele_number_max 2 --max_iters 100 --stop_value

**--allele_number_max** The maximum copy number of each allele allows to take.

**--priors_file_name** Path to the file of the prior distribution. The prior file must be consistent with the --allele_number_max. If not
provided, use uniform prior, which is recommended.
**--priors** Path to the file of the prior distribution. The prior file must be consistent with the --allele_number_max. If not provided,
use uniform prior, which is recommended.

**--max_iters** Maximum number of iterations for training.

Expand All @@ -149,7 +149,7 @@ $ PyLOH.py BAF_heatmap BASENAME

Output files
------------
**\*.PyLOH.counts** The preprocessed paired counts file. It which contains the allelic counts information of sites, which are heterozygous
**\*.PyLOH.counts** The preprocessed paired counts file. It contains the allelic counts information of sites, which are heterozygous
loci in the normal genome. The definition of each column in a *.PyLOH.counts file is listed here:

| Column | Definition |
Expand All @@ -160,26 +160,27 @@ loci in the normal genome. The definition of each column in a *.PyLOH.counts fil
| tumor_A | Count of bases match A allele in the tumor sample |
| tumor_B | Count of bases match B allele in the tumor sample |

**\*.PyLOH.segments** The preprocessed segments file. It which contains the genomic information of each segment. The definition of each
**\*.PyLOH.segments** The preprocessed segments file. It contains the genomic information of each segment. The definition of each
column in a *.PyLOH.segments file is listed here:

| Column | Definition |
| :--------------- | :-------------------------------------------------------- |
| seg_name | Name of the segment |
| chrom | Chromosome of the segment |
| start | Start position of the segment |
| end | End position of the segment |
| normal_reads_num | Count of reads mapped to the segment in the normal sample |
| tumor_reads_num | Count of reads mapped to the segment in the normal sample |
| LOH_frec | Fraction of LOH sites in the segment |
| log2_ratio | Log2 ratio between tumor_reads_num and normal_reads_num |
| Column | Definition |
| :--------------- | :---------------------------------------------------------------------- |
| seg_name | Name of the segment |
| chrom | Chromosome of the segment |
| start | Start position of the segment |
| end | End position of the segment |
| normal_reads_num | Count of reads mapped to the segment in the normal sample |
| tumor_reads_num | Count of reads mapped to the segment in the normal sample |
| LOH_frec | Fraction of LOH sites in the segment |
| LOH_status | FALSE -> no LOH; TRUE -> significant LOH; UNCERTAIN -> medium level LOH |
| log2_ratio | Log2 ratio between tumor_reads_num and normal_reads_num |

**\*.PyLOH.segments.extended** The extended segments file after run_model. There are two additional columns:

| Column | Definition |
| :--------------- | :-------------------------------------------------------- |
| allele_type | Estimated allele type of the segment |
| copy_number | Estimated copy number of the segment |
| Column | Definition |
| :--------------- | :-------------------------------------|
| allele_type | Estimated allele type of the segment |
| copy_number | Estimated copy number of the segment |

**\*.PyLOH.purity** Estimated tumor purity.

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