Different sources name decoys inconsistently ( >phiX174 vs. >gi|9626372|ref|NC_001422.1| ). Aligners see them as different sequences → different mapping outcomes.
| Feature | Specification | | :--- | :--- | | | GRCh37 (hg19) | | Source | 1000 Genomes Project (Phase 2) | | Decoy Sources | Human herpesvirus 4 (EBV), phiX174, E. coli str. K-12, Saccharomyces cerevisiae , and more | | Total Contigs | ~93 (including primary + decoy) | | File Size | Approximately 3.2–3.5 GB (compressed .gz) | | MD5 Checksum (Typical) | Varies by source; always verify post-download | download human-g1k-v37-decoy.fasta
gatk CreateSequenceDictionary -R human_g1k_v37_decoy.fasta | Feature | Specification | | :--- |
If using GATK, create a dictionary using Picard: java -jar picard.jar CreateSequenceDictionary R=human-g1k-v37-decoy.fasta O=human-g1k-v37-decoy.dict . Conclusion Conclusion You can download the reference genome and
You can download the reference genome and its associated decoy files from the following authoritative sources:
After downloading, you must prepare the file for use in bioinformatics pipelines like GATK or BWA. Decompress gunzip hs37d5.fa.gz Index for SAMtools samtools faidx hs37d5.fa Create a Sequence Dictionary (for GATK/Picard) gatk CreateSequenceDictionary -R hs37d5.fa Index for BWA (if aligning) bwa index hs37d5.fa 4. Key Differences to Note