Status Column not present in _CNVs file

[paurods]

Hello,

I have used the following config file:

[general]
chrLenFile = /media/prodriguez/disk1/Databases/genomes/Hsapiens/hg19/seq/chromosomes/hg19.fa.fai
window = 0
ploidy = 2,3
outputDir = /media/prodriguez/disk1/data/prodriguez/Projects/RISC3CAT_cfDNA/tests/test_FREEC

#sex=XY
breakPointType=4
chrFiles =  /media/prodriguez/disk1/Databases/genomes/Hsapiens/hg19/seq/chromosomes

maxThreads=6

breakPointThreshold=1.2
noisyData=TRUE
printNA=FALSE

readCountThreshold=50

[sample]

mateFile = /media/prodriguez/disk1/data/prodriguez/Projects/RISC3CAT_cfDNA/Analysis/615/work/align/615_tumor/615_tumor-sort.bam
inputFormat = bam
mateOrientation = FR

[control]

mateFile = /media/prodriguez/disk1/data/prodriguez/Projects/RISC3CAT_cfDNA/Analysis/615/work/align/615_normal/615_normal-sort.bam
inputFormat = bam
mateOrientation = FR

[BAF]

makePileup = /media/prodriguez/disk1/data/prodriguez/Projects/RISC3CAT_cfDNA/Analysis/615/final/2018-07-12_615/615-germline-ensemble-annotated.vcf.gz
minimalCoveragePerPosition = 5
fastaFile = /media/prodriguez/disk1/Databases/genomes/Hsapiens/hg19/seq/hg19.fa

[target]

captureRegions = /media/prodriguez/disk1/data/prodriguez/Projects/RISC3CAT_cfDNA/Analysis/615/work/bedprep/cleaned-MedExome_hg19_empirical_targets.Plus75.intervals_pluschr.bed

As I have used BAF and control options, according to documentation, I expect to find Status and CNA/LOH columns in the _CNVs file. Nevertheless, I cannot find these columns.

Any idea of what is happening?

Thank you in advance,

Pau.

[valeu]

Dear Pau,

You may try to replace makePileup = /media/prodriguez/disk1/data/prodriguez/Projects/RISC3CAT_cfDNA/Analysis/615/final/2018-07-12_615/615-germline-ensemble-annotated.vcf.gz by

SNPfile = 00-common_all.vcf.gz 
makePileup = 00-common_all.vcf.gz 

where 00-common_all.vcf.gz is a file with all possible SNPs, which you can download, for example, for hg19 from ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-common_all.vcf.gz

[HugoMananet]

Hello,

I have the same problem as Pau, following your advice i now use

SNPfile = 00-common_all.vcf.gz
makePileup = 00-common_all.vcf.gz

But i still can't get CNA/LOH and germline/somatic Status columns.

I work on WES data with controlfreec v11.6.

My config file contains this :

[general]

chrLenFile = /path/tools/controlfreec/ucsc.hg19.fasta.fai
window = 0
ploidy = 2,3,4
outputDir =/path/data/controlfreec_v11.6_results/
breakPointType = 4
chrFiles = /path/references/hg19/ucsc/chromosomes/
degree = 1
bedtools = bedtools
maxThreads = 6
breakPointThreshold = 1.2
noisyData = TRUE
printNA = FALSE
readCountThreshold = 50
minimalSubclonePresence = 0.3
forceGCcontentNormalization = 1
gemMappabilityFile = /path/tools/controlfreec/out100m1_hg19.gem
uniqueMatch = TRUE
contaminationAdjustment = TRUE
intercept = 0
telocentromeric = 50000

[sample]

mateFile = /path/data/sample_sorted_dedup_bam_realigned_recal.bam
inputFormat = bam
mateOrientation = 0

[control]

mateFile = /path/data/control_sorted_dedup_bam_realigned_recal.bam
inputFormat = bam
mateOrientation = 0

[BAF]

SNPfile = /path/tools/controlfreec/00-common_all_chr.vcf.gz
minimalCoveragePerPosition = 5
minimalQualityPerPosition = 0
makePileup = /path/tools/controlfreec/00-common_all_chr.vcf.gz
fastaFile = /path/references/hg19/ucsc/ucsc.hg19.fasta

[target]

captureRegions = /path/manifests/exome_somatic/Manifest_exome.bed

Any ideas as to what i'm doing wrong ?

Thank you in advance

Hugo

[valeu]

Hi Hugo, I would need the complete output into the command line to see where the issue could be.