I am trying to run VarScan with readcounts option, but I keep getting this error
This is the command I'm using:
Can you please help me?
Thanks
Reading input from /users/fg253/new_data_drug_resistance/Co89-2/remapping_to_reference/out.sorted.rmdup.bam.mpileup
Error: Invalid format for pileup at line null
EK12AG100 1438119 T 0
Error: Invalid format for pileup at line null
EK12AG100 1438119 T 0
java -jar $SW_DIR/VarScan.v2.3.6.jar readcounts $MPILEUP --min-base-qual 20 --output-file $READCOUNTS_VCF
Thanks