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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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Somatic CNVs #109

Open Akazhiel opened 2 years ago

Akazhiel commented 2 years ago

Hello!

I'm attempting to run the tool with a matched tumor-normal sample but the _CNVs file that produces is lacking the end coordinate and the somatic/germline classification.

This is the config file I'm using to run the tool:

[general]
BedGraphOutput = TRUE
chrFiles = /input/references/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes
chrLenFile = /input/hg19.fai
forceGCcontentNormalization = 1
maxThreads = 40
minimalSubclonePresence = 100
ploidy = 2
sex = XX
readCountThreshold = 50
breakPointThreshold = 1.2
breakPointType = 4
coefficientOfVariation = 0.05
gemMappabilityFile = /input/out100m2_hg19.gem
noisyData = TRUE

[control]
inputFormat = pileup
mateFile = /input/CABA_Nomal.pileup
mateOrientation = FR

[sample]
inputFormat = pileup
mateFile = /input/CABA_Tumor.pileup
mateOrientation = FR

[BAF]
SNPfile = /input/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf

[target]
captureRegions = /refs/S07604514_hs_hg19_Padded.bed

And this is a snippet of the _CNVs file

1       210111420       1       3       gain    -       -1
2       224740  2       3       gain    AAB     0.552902
2       10183716        2       3       gain    AAB     1.79574
2       10952590        2       3       gain    AAB     0.580177
2       26395942        2       3       gain    AAB     0.383094
2       32713514        2       2       neutral AA      100
2       32819956        2       3       gain    AAB     0.677852
2       42795780        2       3       gain    AAB     0.321705
2       55599384        2       4       gain    -       -1
2       55645809        2       3       gain    AAB     1.10152

Looking forward to hearing from you.

Thanks, Jonatan

Edit: Attached the stdout and stderr from the tool.

freec_paired_output.txt

valeu commented 2 years ago

Dear Jonatan, I went through the code and I don't understand why FREEC is printing it this way.. And it is the first time I see this issue, which is quite surprising given that you use a good configuration of parameters. One thing you could try is to delete or comment "forceGCcontentNormalization = 1" and see whether you don't get a better output with this.