The pipeline requires multiple files that must be downloaded and placed in the config file before running the pipeline.
| File | URL |
|---|---|
| genome | https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz |
| dbsnps | ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/dbsnp_146.hg38.vcf.gz |
| known-indels | https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz |
| 1000g_phase1 | https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz |
| gnomad | https://storage.googleapis.com/gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz |
| contamination | https://storage.googleapis.com/gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz |