Targeted Analysis¶

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: - First column indicates the chromosome of the desired region to analyze - Second and Third columns are the start and end positions of the region respectively.

sample.bed

chr1   56091000    56092000
chr5   37281200    37291200
chr8   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 --reference ref.fasta \
    --tumor tumor.bam --normal normal.bam \
    --bed-file sample.bed --out-vcfgz output.vcf.gz