Pindel - geno tags

Question

[pao272]

Hi, I'm working with Pindel for indel calling and utilizing a config file to feed the program a normal and tumour bam file. I've noticed a few errors with the genotyping information the program is providing and it appears to be missing some information regarding to read coverage. Specifically, I am looking to add genotype flags control & tumour read coverage, reads reporting the variant, and reads reporting variant in both directions. Below is the command I pass the module. The config_file is a .txt file containing the information for the control and tumour bam.

pindel -T 5 -f $reference -i $config_file -c ALL -o $output
pindel2vcf -P $1 -r $reference -R WBcel235/ce11 -d 20130201 -v $output/$1_all.vcf

Thanks