logfile.log

# example run :
perl bionanotator.pl --i ../bionanotator_germline_infile.csv --del 0 --sample testrun_46_g --c g --include 1,3,11
perl bionanotator.pl --i ../somativ_bionano_output_raw.csv --del 0 --sample testrun_46_s --c s  --include 1,3,11
perl bionanotator.pl --i ../somativ_bionano_output_raw.csv --del 0 --sample testrun_39_s --c s
perl bionanotator.pl --i ../test1_bnout_raw.csv --del 0 --sample testrun_39_g --c g
perl bionanotator.pl --i ../test1_bnout_raw.csv --del 0 --sample test
bionanotator$ perl bionanotator.pl --i ../bionano_out_new.vcf --del 0 --sample testrun_5

reading hallmark mapping file hallmark_genes.tsv...
found infile. creating rundir...
created run dir run_testrun_29
now in run_testrun_29/.
executed annovar:
set to not delete annovar in-between files.
found annovar outfile: testrun_29.annotated.hg38_multianno.txt
found  NO allele frequencies, thus excluding them ...
done preparing annotated file :
errors bedtools execution:
errors cutting the bedtools outfile:
errors pasting the complete outfile: