Customizing your VCFs

Adding strains is straightforward. Simply add a file in standard Variant Call Format to the /name/of/strain/vcf/db/ directory.

/name/of/strain/vcf/db
|--strain1.vcf
|--strain2.vcf
|--strain3.vcf
|--strain4.vcf

Formatting

Make sure that at minimum, you include a header with VCF version and "contig" or chromosome info at the top. For examples, see the pregenerated hg19_VCF reference VCFs.

##fileformat=VCFv4.2
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
...
##contig=<ID=chrM,length=16571>
##contig=<ID=chrUn_gl000226,length=15008>
##contig=<ID=chr18_gl000207_random,length=4262>
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
chr6    117715410   .   C   A   0   PASS    .
chr8    27690580    .   C   G   0   PASS    .
chr11   66616566    .   G   A   0   PASS    .
chr11   125875659   .   G   C   0   PASS    .
...

caution

Genome build is important to note here. Make sure your VCF file is based on the same genome build as your BAM file and that the contig/chr names match the VCF headers.

Custom DepMap set (hg38)

If you are interested in several human cell line not available in the pregenerated sets, consider using the provided scripts to download and formats the variants in DepMap for all cell lines in Model.csv. To avoid downloading the full set, you could update Model.csv to only contain the rows you are interested in. Note that Model.csv was last pulled on May 14, 2023 and new cell lines may have been added to DepMap since. Redownload Model.csv to get the latest.

note

While Model.csv might be out of date as a list of cell lines, the variants pulled are the most recent at the time of the script's execution. Only update Model.csv if there is a newly added cell line that is missing. To update variants, simply re-execute the script.