pecgs-cnv

cwl wrapper for dinglab somatic cnv pipeline based on GATK4 workflow

based on dinglab cnv pipeline

Step 1 (optional): Creating pool of normals (PON) on compute1.

Only do this step if you need a new pool of normals. One has already been created from 86 CPTAC bams here /storage1/fs1/dinglab/Active/Projects/estorrs/pecgs-resources/cnv_resources/pon/create_pon/gatk4scnaPON.Normal.hdf5

notebook for creating pon commands on compute1

Step 2: Get somatic CNV for sample.

notebook for generating test CNV commands

notebook for generating commands to run cwl on compute1

directory containing commands to run cnv for a sample on compute1

Running cnv.py

Arguments

usage: cnv.py [-h] [--out-dir OUT_DIR] [--gene-level-script GENE_LEVEL_SCRIPT] [--merge-gene-script MERGE_GENE_SCRIPT] [--genome GENOME] [--genome-dict GENOME_DICT] [--target-interval-list TARGET_INTERVAL_LIST] [--common-biallelic COMMON_BIALLELIC] [--protein-coding-gene PROTEIN_CODING_GENE] [--pool-of-normals POOL_OF_NORMALS] sample tumor_bam normal_bam

positional arguments:

• sample
  • Sample id
• tumor_bam
  • wxs tumor bam
• normal_bam
  • wxs normal bam

optional arguments:

• -h, --help

  • show this help message and exit

• --out-dir OUT_DIR

  • output directory

• --gene-level-script GENE_LEVEL_SCRIPT

  • location of gene level python script from https://github.com/ding-lab/GATK4SCNA/tree/main/src. included in cnv/ dir.

• --merge-gene-script MERGE_GENE_SCRIPT

  • location of merge gene level python script from https://github.com/ding-lab/GATK4SCNA/tree/main/src. included in cnv/ dir.

• --genome GENOME

  • reference location

• --genome-dict GENOME_DICT

  • reference .dict location

• --target-interval-list TARGET_INTERVAL_LIST

  • location of IDT_xGen_Exome_Research_Panel_v1.hg38.removed_alt_chr.bed.target.preprocessed.exome.interval_list

• --common-biallelic COMMON_BIALLELIC

  • location of af-only-gnomad.hg38.common_biallelic.chr1-22XY.vcf

• --protein-coding-gene PROTEIN_CODING_GENE

  • location of gencode.v34.annotation.gene_filterd.need_gene_symbol.no_sym.filtered_to_hgnc_protein-coding_genes.bed

• --pool-of-normals POOL_OF_NORMALS

  • location of pool of normals created in step 1 and 2 of https://github.com/ding-lab/GATK4SCNA/tree/main/src. available at /storage1/fs1/dinglab/Active/Projects/estorrs/pecgs-resources/cnv_resources/pon/create_pon/gatk4scnaPON.Normal.hdf5

Docker

docker image is available from dockerhub (estorrs/pecgs_cnv:0.0.1)