Generate the Panel of Normal files for TNseq and TNscope.
Du kan inte välja fler än 25 ämnen Ämnen måste starta med en bokstav eller siffra, kan innehålla bindestreck ('-') och vara max 35 tecken långa.
YaqingLiu 6a1550682f Update: README.md 4 år sedan
tasks Fix bug: tumor_sample parameter 4 år sedan
.DS_Store Alter: test 4 år sedan
README.md Update: README.md 4 år sedan
defaults update input 4 år sedan
inputs Fix bug: inputs 4 år sedan
workflow.wdl Fix bug: tumor sample SM tag is not present in the bam file 4 år sedan

README.md

Panel of Normals

The Panel of Normals approach uses a set of matched normal samples to determine the baseline level from which to call CNV events. These matched normal samples should be derived from the same library prep and sequencing workflow that was used for the case sample. This allows the algorithm to subtract out system level biases that are not sample specific.

Getting Started

We recommend using choppy system and Aliyun OSS service. The command will look like this:

# Activate the choppy environment
$ open-choppy-env

# Install the APP
$ choppy install YaqingLiu/PoN-latest [-f]

# List the parameters
$ choppy samples YaqingLiu/PoN-latest [--no-default]

# Submit you task with the `samples.csv file` and `project name`
$ choppy batch YaqingLiu/PoN-latest samples.csv -p Project [-l project:Label]

# Query the status of all tasks in the project
$ choppy query -L project:Label | grep "status"