VarScan- invalid format for pileup

[RBCT]

Hello,

I've used the following command to filter my BAM file, run samtools pileup and varscan:

samtools view -b -q 10 myBam.bam | samtools mpileup -f myRef.fasta -
| java –jar VarScan.v2.3.6.jar pileup2snp --min-coverage 6 --min-avg-qual 4 --min-var-freq 0.01 --p-value 0.05

The program ran for a while and then I got this error:

Error: Invalid format for pileup at line 820808910
chr18 74082743

It seems like a lot of people have had this issue before but I don't know how to fix it. Any help will be greatly appreciated. Thanks!!

[nnutter]

I can't really offer any help but it might be useful to split that pipe of three commands into separate steps so you can figure out which tool is throwing the error.