Targeted Scan

Lancet can be run on exome/panel data by providing a preselected list of regions along the genome with a BED file. The BED file is a tab delimited text file which must contain at least three columns in the following order: the first column indicates the chromosome of the desired region to analyze and the second and third columns are the start and end positions of the region respectively.

sample.bed:

1   56091000    56092000
5   37281200    37291200
8   11200000    11300000

In the example above the sample.bed file can be used to call variants in chromosomes 1, 5, and 8 from positions 56091000-56092000, 37281200-37291200, and 11200000-11300000 respectively using the following command:

lancet2 pipeline -t tumor.bam -n normal.bam -r ref.fasta -o out.vcf -b sample.bed

note

Chromosome labels in the BED file must match the chromosome labels present in the genome reference and BAM files.