Correct options for CNVnator

dfermin315 · 06-19-2019, 07:25 AM

Greetings,

I'm trying to run CNVnator on a cohort of ~300 BAM files.

For testing purposes I'm trying to run it on just 3 BAM files first.
Here are the commands I'm running:

Code:

export HS37d5=/data/fastas/hs37d5

cnvnator -root chr22.root -genome GRCh37 -chrom 22 -tree \
	/nfs/wgs30x/bam.files/samp1.bam \
	/nfs/wgs30x/bam.files/samp2.bam \
	/nfs/wgs30x/bam.files/samp3.bam;

cnvnator -root chr22.root -genome GRCh37 -chrom 22 -his 1000 -d $HS37D5

cnvnator -root chr22.root -genome GRCh37 -chrom 22 -stat 1000

cnvnator -root chr22.root -genome GRCh37 -chrom 22 -partition 1000

cnvnator -root chr22.root -genome GRCh37 -chrom 22 -call 1000 > chr22.cnvnator.out

Now all of this runs and I don't get an error (as far as I can tell).
The last command I try is:

Code:

cnvnator -pe /nfs/wgs30x/bam.files/samp1.bam \
   /nfs/wgs30x/bam.files/samp2.bam \
   /nfs/wgs30x/bam.files/samp3.bam \
   -qual 20 -over 0.8 -root chr22.root -f chr22.support_reads;

This command never finishes. I left it running for 36 hours and it didn't produce anything.

I believe I'm screwing up the cnvnator -pe command but I can't figure out what the correct command should be.

Using the cnvnator2VCF.pl produces a VCF file but it doesn't contain any read count information.

Does anyone have any suggestions as to what I'm doing wrong?
In case it helps I'm using CNVnator v0.4 (latest download from github).
The system is a RHEL 7.2 box fully patched.

Thank you in advance for any and all help.

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06-19-2019, 07:25 AM	#1
dfermin315 Junior Member Location: Michigan, US Join Date: Mar 2017 Posts: 4	Correct options for CNVnator Greetings, I'm trying to run CNVnator on a cohort of ~300 BAM files. For testing purposes I'm trying to run it on just 3 BAM files first. Here are the commands I'm running: Code: export HS37d5=/data/fastas/hs37d5 cnvnator -root chr22.root -genome GRCh37 -chrom 22 -tree \ /nfs/wgs30x/bam.files/samp1.bam \ /nfs/wgs30x/bam.files/samp2.bam \ /nfs/wgs30x/bam.files/samp3.bam; cnvnator -root chr22.root -genome GRCh37 -chrom 22 -his 1000 -d $HS37D5 cnvnator -root chr22.root -genome GRCh37 -chrom 22 -stat 1000 cnvnator -root chr22.root -genome GRCh37 -chrom 22 -partition 1000 cnvnator -root chr22.root -genome GRCh37 -chrom 22 -call 1000 > chr22.cnvnator.out Now all of this runs and I don't get an error (as far as I can tell). The last command I try is: Code: cnvnator -pe /nfs/wgs30x/bam.files/samp1.bam \ /nfs/wgs30x/bam.files/samp2.bam \ /nfs/wgs30x/bam.files/samp3.bam \ -qual 20 -over 0.8 -root chr22.root -f chr22.support_reads; This command never finishes. I left it running for 36 hours and it didn't produce anything. I believe I'm screwing up the cnvnator -pe command but I can't figure out what the correct command should be. Using the cnvnator2VCF.pl produces a VCF file but it doesn't contain any read count information. Does anyone have any suggestions as to what I'm doing wrong? In case it helps I'm using CNVnator v0.4 (latest download from github). The system is a RHEL 7.2 box fully patched. Thank you in advance for any and all help.