Use MicroSec for FFPE filtering. ffpefilter pipeline is a pipeline designed to do variant filtering for FFPE samples by using microsec tool. It uses the docker image scao/microsec:0.0.1 for efficiently launching jobs on compute1 cluster (LSF job system)
The only thing you need to do is to do "git clone https://github.com/ding-lab/ffpefiltering.git"
-
Create folder (rdir or use anyname you like) for running multiple samples
-
Create subdirectory under rder for each sample that need to run ffpe filtering
For each sample direcotry, it should contain a maf file and a tumor bam file and associated index file for each sample named as:
samplename.formated.maf
samplename.T.bam
samplename.T.bam.bai
The maf file should contain the following columns, which can be extracted from the original maf file from somaticwrapper pipeline (remember to remove _T for the sample name in the Tumor_Sample_Barcode)
Hugo_Symbol Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 Tumor_Sample_Barcode
SAMD11 chr1 925818 925818 + Intron SNP G G T ALCH-ABBG-TTP1-A
- Enter the folder which contains ffpefilter.pl script, type
perl ffpefilter.pl --rdir --log --groupname --users --step
rdir = full path of the folder holding files for this run (user must provide)
log = full path of the folder for saving log file; usually upper folder of rdir
groupname = job group name
users = user name for job group
step = run this pipeline step by step. (user must provide)
See work_log_alchemist_test for how to submit the jobs.
Yingduo Song and Song Cao