I'm new to the Whole Exome Sequencing analytics and keep running into the following issue -
I'm running Varscan2.4.2 and invoking the copynumber command on an mpileup file and I keep receiving a "parsing exception error":
[mpileup] 2 samples in 2 input files
<mpileup> Set max per-file depth to 4000
Min coverage: 10
Min avg qual: 15
P-value thresh: 0.01
Reading input from Normal.sort.rmdup_Tumor.sort.rmdup.mpileup
Reading mpileup input...
Parsing Exception on line:
chr1 12956 T 0 * * 0
A little info on the pre-processing: I have downloaded Bam files from the TCGA, used Samtools to sort the Bam files, used Picard tools to mark duplicates, samtools to build the mpileup and now running varscan2 for the copy number output.
Anyone have any idea on what could be causing the Parsing Exception error and how I might possibly circumvent this? I've done a little googling and saw that in other cases people have tried removing 0 coverage lines by piping the mpileup through the awk command, but I thought this issue was addressed in the later versions of Varscan.
Thank you kindly for reading!
In case more info is needed, Here are the commands and options I am running:
samtools sort -l 0 -O bam -T Normal.sort -o Normal.sort.bam Normal.bam
samtools sort -l 0 -O bam -T Tumor.sort -o Normal.sort.bam Tumor.bam
java -jar Picard.jar MarkDuplicates I=Normal.sort.bam O=Normal.sort.mkdp.bam METRICS_FILE=dup1 TMP_DIR=tmp1
java -jar Picard.jar MarkDuplicates I=Tumor.sort.bam O=Tumor.sort.mkdp.bam METRICS_FILE=dup2 TMP_DIR=tmp2
samtools mpileup -q 1 -B -f GRCh38.d1.vd1.fa Normal.sort.mkdp.bam Tumor.sort.mkdp.bam > Normal.sort.mkdp_Tumor.sort.mkdp.mpileup
java -jar VarScan.v2.4.2.jar copynumber Normal.sort.mkdp_Tumor.sort.mkdp.mpileup Normal.sort.mkdp_Tumor.sort.out --mpileup 1 --data-ratio 0.8916044227