#3 Copynumber gives gc content>100 and error in Copycaller

[bapelsin]

Hi,

Im using VarScan.v2.3.2 to do CNV analysis on HighSeq exome data from tumor-normal pairs. When running copynumber, all appears ok, but when filtering the resulting .copynumber file using Copycaller, I get an error ("Parsing Exception", please see below).

When running VarScan copynumber like this:
java -jar /VarScan.v2.3.2.jar copynumber $NOR $TUM $BASENAME

I got the following output:
########
Normal Pileup: /177_1N.prmdup.realign.recal_sorted.mpileup
Tumor Pileup: /177_1T.prmdup.realign.recal_sorted.mpileup
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Not resetting normal file because chrM < chrY
561343988 positions in tumor
557785077 positions shared in normal
38214383 had sufficient coverage for comparison
482476 raw copynumber segments with size > 10
474997 good copynumber segments with depth > 10
##########

So we have an error stating "Not resetting normal file because chrM < chrY".

I saw an answer that dkobolt had given regarding this error message saying that "This is just a warning printed by VarScan as it's simultaneously parsing normal and tumor files. As long as your output files contain all of the chromosomes that you expect, you can safely ignore it."

So I double checked and all chromosomes are present in the copynumber file.

Then I ran Copycaller like this:
java -jar /VarScan.v2.3.2.jar copyCaller $IN --output-file ${IN}.called

The output I get from the CopyCaller is the following:
#####################
Min coverage: 20
Reading input from /177_1T.copynumber
Parsing Exception on line:
chr1 10010 10109 100 30,4 28,4 -0,097 51,0
For input string: "30,4"
Error parsing input: null
java.lang.NullPointerException
at net.sf.varscan.CopyCaller.<init>(CopyCaller.java:293)
at net.sf.varscan.VarScan.copyCaller(VarScan.java:344)
at net.sf.varscan.VarScan.main(VarScan.java:173)

##################
I am not sure what is wrong with this line, however when looking at the output from "copynumber" I noticed that the GC content sometimes exceeds 100, please see attached picture.

I would be greatful for any input on how to solve this!
Thank you in advance!

[bapelsin]

Copynumber file