VarScan2 copynumber option error

[curious2]

VarScan2 seems to be a great program, and I especially am interested in trying out the "copynumber" option. I have run it many times with success with the "somatic" option, but when I switch to "copynumber", it fails.

Here is one example (made quickly to document from some shortened mpileups) where it works for "somatic" but crashes for "copynumber":

[TRY4]$ java -jar /CODE/VarScan.v2.3.5.jar somatic shortX16normal.mpileup shortX15tumor.mpileup shortTRY4 --min-var-freq 0
Normal Pileup: shortX16normal.mpileup
Tumor Pileup: shortX15tumor.mpileup
Min coverage: 8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2: 1
Min var freq: 0.0
Min freq for hom: 0.75
Normal purity: 1.0
Tumor purity: 1.0
Min avg qual: 15
P-value thresh: 0.99
Somatic p-value: 0.05
INS-1-C failed with 1 13
INS-1-T failed with 1 14
INS-1-A failed with 1 14
.
.
.
INS-1-C failed with 1 13
INS-1-T failed with 1 14
INS-1-T failed with 1 13
65597 positions in tumor
65530 positions shared in normal
42830 had sufficient coverage for comparison
42395 were called Reference
0 were mixed SNP-indel calls and filtered
303 were called Germline
2 were called LOH
125 were called Somatic
5 were called Unknown
0 were called Variant

Then I run VarScan with the "copynumber" option and receive an error:

[TRY4]$ java -jar /CODE/VarScan.v2.3.5.jar copynumber shortX16normal.mpileup shortX15tumor.mpileup shortCNTRY4
Normal Pileup: shortX16normal.mpileup
Tumor Pileup: shortX15tumor.mpileup
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5
at net.sf.varscan.Copynumber.<init>(Copynumber.java:693)
at net.sf.varscan.VarScan.copynumber(VarScan.java:301)
at net.sf.varscan.VarScan.main(VarScan.java:193)
[TRY4]$



I have tried this several times now, including with different versions of VarScan2 and samtools. Another error I get sometimes is:


[CNtry2_397]$ java -jar /tomato/job/ccm13/VarScan.v2.3.5.jar copynumber try2_TandN.mpileup --mpileup 1
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Reading input from try2_397.mpileup
Reading mpileup input...
Parsing Exception on line:
chr1 13959 C 2 ,, ;G 0
8
[CNtry2_397]$


This one appears to happen at the first time there is a 0 read occurrence (do those need to be taken out from the mpileups - and if so, why are they in there?)

Thanks very much for any help or suggestions!

[chumho]

VarScan2 copynumber crashed

I encountered the same problem for VarScan 2.3.5 on Linux. Any clue?
Eric.

[dkoboldt]

Hello, and thanks for posting this issue. Yes, VarScan does not expect to see a line with coverage=0 in a single-sample pileup file. VarScan v2.3.6 addresses this issue and should not crash. In either case, I recommend using two-sample mpileups for normal/tumor comparisons (somatic and copynumber), but doing so with the -B parameter (in samtools mpileup) to disable BAQ computation.

[pmint]

solution

...........

[sophiespo]

Hi Dan,

I was wondering if you could help me. I've been trying to get this particular aspect of VarScan2 working for a while.

I am creating my pileup then running VarScan like this:

samtools mpileup -B -q 1 -f reference.fa normal.bam tumour.bam > sample.mpileup

java -jar VarScan.v2.3.6.jar copynumber sample.mpileup output --mpileup 1

but I am still getting an error:

Min coverage:	10
Min avg qual:	15
P-value thresh:	0.01
Reading input from sample.mpileup
Reading mpileup input...
Parsing Exception on line:
chr1	3038588	c	0	*	*	0		
8

I am using a two-sample pileup and the -B flag like you've said, am I missing something?

Thanks
Sophie

[sophiespo]

Hello? @dkoboldt

[brdido]

Hello,

i'm using separated mpileup (normal and tumoral) with -B option and VarScan 2.3.6 and getting the error :

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException

The error goes away if i don't use a reference fasta file in mpileup command (-f).

I've rebuilt the index for fasta files and still getting the same error...

Any help or ideas would be great. i'm running mpilup again with no reference file just for copynumber pipeline for now...

[brdido]

In my last post i said that running mpileup without a reference worked fine. This is not true. It only happened in a sample file. When I started to run the other samples the same error happened.

[brdido]

I've opened source code in v2.3.6 and the code expects 5 columns. But my mpileup has only 4 columns when coverage is 0 (no qualities)

I'm cleaning my mpileup files to see what happens.

[aditisk]

@brdido, were you able to solve the issue ? I am facing a similar problem with my samples.

[brdido]

aditisk:
at first i changed mpileup files to make it "compatible". But for whole genomes it could take a lot of time so i changed the source code an rebuilt .jar file.

Have you tested v2.4.1?

https://github.com/dkoboldt/varscan