CNVKit for unmatched tumor-only WGS samples

Question

[vctrm67]

Does anyone know how to use cnvkit on tumor-only WGS samples? I tried making a flat reference using b37 but I cannot without a target/antitarget bed file, which I don't have for an entire genome.

[igor]

Did you check the docs? https://cnvkit.readthedocs.io/en/stable/nonhybrid.html

[vctrm67]

Yes. There is no mention of what to do for this specific case.

[igor]

Isn't this what you are looking for?

The batch --method wgs option uses the given reference genome’s sequencing-accessible regions (“access” BED) as the “targets” – these will be calculated on the fly if not provided. No “antitarget” regions are used.

[vctrm67]

I looked at that, but you can see that they use the -n tag, whereas I do not have any normals. I need to use the -r tag:

  -r REFERENCE, --reference REFERENCE
                        Copy number reference file (.cnn).

However, I cannot seem to generate a .cnn file without a target/antitarget file, which I don't have since this is WGS and I can't find one for b37.

[lakhujanivijay]

vctrm67

Were you able to find a solution for this ?

[rohitsatyam102]

Yeah, I am also stuck with it. Did anyone here find a way?

[Pedro]

Hi everyone,

We did the following:

#!/bin/sh

# This script will create the following files in
# 1. Present Working Directory (PWD):
# - access.hg38.bed
# - antitargets.hg38.bed
# - FlatReference.cnn
#
# 2. /PWD/batch1:
# - BAM_FILE_1.antitargetcoverage.cnn
# - BAM_FILE_1.targetcoverage.cnn
# - BAM_FILE_2.antitargetcoverage.cnn
# - BAM_FILE_2.targetcoverage.cnn
# ...
# - BAM_FILE_N.antitargetcoverage.cnn
# - BAM_FILE_N.targetcoverage.cnn

# Set CORES = to your machine or if less, number of BAM files.
CORES=64

TARGET=/PATH_TO/Exome-Agilent_V6.bed
FASTA=/PATH_TO/hg38.fa
DIR=/PATH_TO/WES/BAM/

cnvkit.py access $FASTA --output access.hg38.bed

cnvkit.py antitarget ${TARGET} --access access.hg38.bed --output antitargets.hg38.bed

cnvkit.py reference --output FlatReference.cnn --fasta $FASTA --targets ${TARGET} --antitargets antitargets.hg38.bed

cnvkit.py batch ${DIR}/*.bam --reference FlatReference.cnn \
            --output-dir batch1 \
            --diagram --scatter -p ${CORES}