MethylPurify 2.0-20141116

Description:

MethylPurify 2.020141116

This script is used for predicting subclone purity.

Get Dependent data
Get the version of genome fasta that you mapped your fastqs,
we support hg18 and hg19 genome fasta now, take hg19 as an example
## use built-in script
cd methylpurify/db
bash genome.sh hg19


Get Dependent software

samtools, version 0.2.0
numpy, version 1.8.2
pyfasta, version 0.5.2



Easy to start
Input: BAM file, this should be mapped with BSMap with -R option
* BSMap
Currently, we only support hg19 and hg18 genome index mapped BAM file.
If your fastq mapping is done with hg19 index, use following command:
MethylPurify -f input.bam -b 300 -c 10 -s 50 -i methylpurify/db/CGI_hg19_slop1000.bed -g /path/to/hg19.fa --cnv
The results would be placed into input folder: alpha1.pred, MethylProfile.bed


Options

-f: input BAM file
-c: coverage level
-b: genome bin size
-s: sampling times
-g: species genome fasta file
-i: CG island specified, can use methylpurify/db/CGI_hg19_slop1000.bed for hg19, methylpurify/db/CGI_hg18_slop1000.bed for hg18
–cnv: use cnv data or not, only available for hg19, for other assembly, do not use this