I'm trying to go through the Varscan2 protocol 1 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4278659/); however I am getting "Too many parsing exceptions encountered; exiting" at the step of filtering SNP calls to remove those near indel positions (VarScan.jar filter). Does anyone have any idea what I should be looking into? Any idea is appreciated!

I use samtools-1.2 to get the mpileup file:

samtools mpileup -B -q 1 -f $referenceFasta $sample.bam > $sample.mpileup

Then run varscan:

java -jar VarScan.v2.3.9.jar mpileup2snp $sample.mpileup \
    --mincoverage 8 \
    --min-var-freq 0.20 \
    --p-value 0.1 \
    >$sample.varScan.snp

java -jar VarScan.v2.3.9.jar mpileup2indel $sample.mpileup \
    --mincoverage 8 \
    --min-var-freq 0.10 \
    --p-value 0.1 \
    >$sample.varScan.indel

The problem occurs here:

printf "\nRun varscan filter\n"
java -jar VarScan.v2.3.9.jar \
filter $sample.varScan.snp \
--indel-file $sample.varScan.indel \
--output-file $sample.varScan.snp.filter

I got the following:

Run varscan filter
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 sample1.varScan.snp
Parsing Exception on line:
chrM    297 A   G   G:17:0:17:100%:4.2852E-10   Pass:0:0:15:2:1E0   0   0   1   0   G:17:0:17:100%:4.2852E-10
For input string: "G:17:0:17:100%:4.2852E-10"
Parsing Exception on line:
chrM    1007    T   C   C:452:85:365:81.11%:1.1083E-169 Pass:29:56:112:253:1E0  0   0   1   0   C:452:85:365:81.11%:1.1083E-169
For input string: "C:452:85:365:81.11%:1.1083E-169"
Parsing Exception on line:
chrM    1813    A   G   G:429:3:423:99.3%:1.5923E-248   Pass:2:1:247:176:1E0    0   0   1   0   G:429:3:423:99.3%:1.5923E-248
For input string: "G:429:3:423:99.3%:1.5923E-248"
Parsing Exception on line:
chrM    2354    C   T   T:1098:2:1080:99.82%:0E0    Pass:1:1:567:513:1E0    0   0   1   0   T:1098:2:1080:99.82%:0E0
For input string: "T:1098:2:1080:99.82%:0E0"
Parsing Exception on line:
chrM    2485    C   T   T:1558:2:1540:99.87%:0E0    Pass:2:0:1058:482:1E0   0   0   1   0   T:1558:2:1540:99.87%:0E0
For input string: "T:1558:2:1540:99.87%:0E0"
Too many parsing exceptions encountered; exiting

In the end after running the supported protocol 1 (bam-readcount and fpfilter), I got 0 variants that passed the filter:

printf "\nRun bam-readcount\n"
bam-readcount/bin/bam-readcount \
-q 1 -b 20 \
-f $referenceFasta \
-l $sample.varScan.snp $sample.bam \
> $sample.varScan.snp.readcounts

printf "\nRun fpfilter.pl\n"
perl varscan_v2.3.9/fpfilter.pl \
$sample.varScan.snp $sample.varScan.snp.readcounts \
-output-basename $sample.varScan.snp.filter