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Methylation subclone detection

Project description

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

Project details


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Files for MethylPurify, version 2.0-20141116
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