Hi,

Can someone inform me on the input requirements for CNVkit? Specifically, in the user manual, they state Gene annotation database, via RefSeq or Ensembl, in BED or “RefFlat” format (e.g. refFlat.txt) [optional] and provide

cnvkit.py batch *Tumor.bam --normal *Normal.bam \
    --targets my_baits.bed --fasta hg19.fasta \
    --access data/access-5kb-mappable.hg19.bed \
    --output-reference my_reference.cnn --output-dir example/

as an example. What is the gene annotation database they refer to? Where can I find one for Human_g1k_v37?

Where can I get the baits bed file that they refer to?