VarScan not resetting normal

[ckr123]

Hi, I am a newbie trying to identify somatic mutations with VarScan. I tried sending the input separately or together and encountered errors for both.

#separate pileup
samtools mpileup -uf RCRS.fa normal.sorted.bam > normal.mpileup
samtools mpileup -uf RCRS.fa tumor.sorted.bam > tumor.mpileup
java -Xmx4g -jar /bin/VarScan.v2.3.5.jar somatic normal.mpileup tumor.mpileup --output-snp sample1.snp --output-indel sample1.indel

Returned messages:
Min coverage: 8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2: 1
Min var freq: 0.2
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
Not resetting normal file because <
Exception in thread "main" java.lang.NumberFormatException: For input string: "iTG,XDP=500;I16=121,361,0,1,12370,335428,17,289,18616,900090,56,3136,8657,185009,25,625;VDB=0.0152PL�����"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:470)
at java.lang.Integer.parseInt(Integer.java:514)
at net.sf.varscan.Somatic.<init>(Somatic.java:1015)
at net.sf.varscan.VarScan.somatic(VarScan.java:282)
at net.sf.varscan.VarScan.main(VarScan.java:188)

#combined pileup
samtools mpileup -uf RCRS.fa normal.sorted.bam tumor.sorted.bam >
mpileup
java -Xmx4g -jar /bin/VarScan.v2.3.5.jar somatic mpileup --mpileup 1 --output-snp sample1.snp --output-indel sample1.indel

Message returned:
Min coverage: 8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2: 1
Min var freq: 0.2
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
Reading input from sample1.mpileup
Reading mpileup input...
Error: Invalid format or not enough samples in mpileup: ï¿ï¿½BC[=��BCFMTNOSM%##samtoolsVersion=0.1.18 (r982:295)

In both cases, I received indel and snp files, but they only have column names. I am really confused.

Thanks,

[dkoboldt]

This issue is caused by the -u parameter given to SAMtools. Remove -u and it should work fine.