VarScan.v2.3.9 filter error p-value

Question

[niggoK]

Hi,

I am getting an error message when I use the VarScan filter option.

Error:

Parsing Exception on line:
chr1    104033  .   T   C   .   PASS    ADP=10;WT=0;HET=0;HOM=1;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    1/1:42:10:10:1:9:90%:5,9538e-5:38:38:1:0:7:2
For input string: "5,9538e-5"

Command:

java -jar VarScan.v2.3.9.jar filter F1_dedup__chr1.VarScan.snp --indel-file F1_dedup__chr1.VarScan.indel --output-filename F1_dedup__chr1.VarScan.snp.filter


Output:

Min coverage:   10
Min reads2: 2
Min strands2:   1
Min var freq:   0.2
Min avg qual:   15
P-value thresh: 0.1
Reading input from /media/data/public_test_samples/test_set/patient_id_12092018/WES/results/varscan/F1_dedup__chr1.VarScan.snp

\#\#fileformat=VCFv4.1
\#\#source=VarScan2
\#\#INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
\#\#INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
\#\#INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
\#\#INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
\#\#INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
\#\#FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
\#\#FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
\#\#FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
\#\#FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
\#\#FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
\#\#FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
\#\#FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
\#\#FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
\#\#FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
\#\#FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
\#\#FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
\#\#FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
\#\#FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
\#\#FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
\#\#FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
\#\#FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
\#CHROM POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Sample1Parsing Exception on line:
chr1    104033  .   T   C   .   PASS    ADP=10;WT=0;HET=0;HOM=1;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    1/1:42:10:10:1:9:90%:5,9538e-5:38:38:1:0:7:2
For input string: "5,9538e-5"
Parsing Exception on line:
chr1    234609  .   T   C   .   PASS    ADP=10;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:22:10:10:4:6:60%:5,418e-3:38:37:3:1:2:4
For input string: "5,418e-3"


Input files:

==> F1_dedup__chr1.VarScan.indel <==
chr1    48966544    .   C   CCT .   PASS    ADP=8;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    1/1:41:8:8:0:8:100%:7,77e-5:0:34:0:0:7:1
chr1    49084615    .   G   GA  .   PASS    ADP=10;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:23:10:10:3:6:60%:4,5249e-3:39:37:3:0:4:2
chr1    49167049    .   TCA T   .   PASS    ADP=8;WT=0;HET=0;HOM=1;NC=0 
...

==> F1_dedup__chr1.VarScan.snp <==
chr1    53634045    .   A   G   .   PASS    ADP=9;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    1/1:46:9:9:0:9:100%:2,0568e-5:0:38:0:0:3:6
chr1    53634172    .   C   T   .   PASS    ADP=13;WT=0;HET=1;HOM=0;NC=0    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    0/1:25:13:13:6:7:53,85%:2,6087e-3:37:36:4:2:3:4
...

I already tried it with the non VCF format and get a similar error.

Thank you for your help.

Kind regards,

Nicolas

[ATpoint]

Please use the formatting bar to indicate code for the future:

[niggoK]

Dear all,

it was the dot, comma decimal problem.

Thanks.

[Sej Modha]

Hi niggoK,

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Answer 1

[Benn]

It seems you are using comma decimal separator, but you should use dot for that.

[ATpoint]

I somewhat remember this error. Think I solved it by adding export LC_ALL=en_US.UTF-8 to the top of ~/.bashrc and then rerun VarScan from the beginning. Also, the latest (and final probably) VarScan version is 2.4.3. You should update.

Answer 2

[niggoK]

Hi guys,

thanks a lot for your very much for your great suggestions.

I reset the language locale settings with "sudo dpkg-reconfigure locales" to "en_US.UTF-8" and now everything is fine.