Usage:

falco 

input:
- bam file
- manifest file
- ref + fai
- locifilt
- manifest

output:
- *.vcf file
- *.qc.ann.txt -> catalog of each assayed bp
- *.qc2.ann.txt -> catalog of transitions
- *.qc.targets.txt -> amplicon centered information, eg depth, start/end positions.

example:

OUTBASE="HCT116-TEST"

## variant calling
falco --bam data/HCT-116/HCT116.bam --output $OUTBASE --ref genome.fa

file1=$OUTBASE".qc.ann.qual.txt"
file2=$OUTBASE".qc2.ann.txt"
file3=$OUTBASE".qc.targets.txt"
file4=$OUTBASE".res.filtered.tsv"

## variant filtering and reporting
falco-filter-report --vcf snpeff.vcf --output $OUTBASE --qc_ann_qual_txt $file1 --qc2_ann_txt $file2 --qc_targets_txt $file3 --res_filtered_tsv $file4