Last updated: Nov 1  2021

The following reference files are used as inputs for the DRAGEN-GATK best practices pipeline, which is implemented in the WARP Whole Germline Single Sample WDL (https://broadinstitute.github.io/warp/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README/). 

These files are used with the hg38 assembly version. 

The Google bucket URIs for reference inputs as well as the relevant code to create the references are listed below. Reference names will match those listed in the WARP Whole Germline Single Sample WDL: https://github.com/broadinstitute/warp/blob/master/pipelines/broad/dna_seq/germline/single_sample/wgs/WholeGenomeGermlineSingleSample.wdl.

**Reference STR table** 
This input is found in the workflows ReferenceFasta struct and is used when building the DragSTR model in GATK. The file only needs to be created once per reference version.

Input name: ref_str
URI: gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.str
Command to create:
    gatk ComposeSTRTableFile \
        -R reference.fasta \
        -O str_table.tsv 

**DRAGMAP reference hash table files**
These references are listed in the DragmapReference struct and are used with the Dragmap aligner.

Input names:
1) hash_table_cmp
2) reference_bin
3) hash_table_cfg_bin

URIs:
1) gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/hash_table.cmp
2) gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/reference.bin
3) gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/hash_table.cfg.bin

Command to create:
    dragen-os \
        --build-hash-table true \
        --ht-reference reference.fasta  \
        --output-directory /home/data/reference/
See the DRAGMAP documentation to download dragen-os and learn more: https://github.com/Illumina/DRAGMAP

**DRAGMAP BED file**
This file is used when creating DRAGMAP reference hash table files with the alt masked BED file and is not a workflow input.

Input name: Not applicable
URI: gs://gcp-public-data--broad-references/hg38/v0/hg38_alt_mask.bed

hg38 masked reference files

URIs:
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.dict
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.64.alt
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.64.amb
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.64.ann
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.64.bwt
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.64.pac
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.64.sa
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.amb
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.ann
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.bwt
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.fai
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.pac
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.sa
gs://gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta.alt

Commands to create:
Mask reference with Ns
	bedtools maskfasta -fi Homo_sapiens_assembly38.fasta -bed \
	hg38_alt_mask.bed -fo Homo_sapiens_assembly38_masked.fasta

Create BWA index
	bwa index Homo_sapiens_assembly38_masked.fasta

Create 64-bit version of BWA index
	bwa index -6 Homo_sapiens_assembly38_masked.fasta

Note that we are using the alt contig masking and  we do not perform any liftover, thus, the liftover file (Homo_sapiens_assembly38_masked.fasta.alt) must be empty.