How do I download HG19?
How do I download HG19?
Download Human Reference Genome (HG19 – GRCh37)
- Download all (GZ) files – chromosomes. Create a directory that will store the downloaded files:
- Uncompress each GZ file – chromosome in the directory. Create a directory that will store the uncompressed files:
- Merge all chromosomes (1, 2, 3, …, X, Y) in one FASTA file.
What is hg19?
The hg19 build is a single representation of multiple genomes. The GRCh Build 38 build provides alternate sequences (“alt_sequences”) for some genomic regions for which their variability prevents adequate representation by one single reference.
What is the difference between GRCm38 and mm10?
The official name for the current mouse reference genome assembly is Genome Reference Consortium Mouse Build 38. It is abbreviated as GRCm38. GRCm38 is referred to as mm10 in the UCSC Genome Browser, but this is not the official assembly name or abbreviation. The GenBank accession for GRCm38 is GCA_000001635.
What is HG19?
What is GRCh38 p13?
GRCh38. p13 is the thirteenth patch release for the GRCh38 reference assembly. No chromosome coordinates changed. This release includes 43 FIX and 2 NOVEL patches. The total number of patch scaffolds is now: 113 FIX and 72 NOVEL.
What is the hg19 reference?
This reference is often referred to as b37 ( Homo_sapiens_assembly19.fasta, MD5sum: 886ba1559393f75872c1cf459eb57f2d ). When people at The Broad Institute’s Genomics Platform refer to the hg19 reference, they are actually referring to b37.
How do we compare SNVs identified based on hg19 vs hg38?
Methods: We conducted analysis comparing the SNVs identified based on HG19 vs HG38, leveraging whole genome sequencing (WGS) data from the genome-in-a-bottle (GIAB) project. First, SNVs were called using 26 different bioinformatics pipelines with either HG19 or HG38.
What is the hg19 reference from the Broad Institute?
When people at The Broad Institute’s Genomics Platform refer to the hg19 reference, they are actually referring to b37. This reference contains some alterations from the baseline reference from the Genome Reference Consortium.
Is the humang1kv37 reference equivalent to B37?
The humanG1Kv37 ( human_g1k_v37.fasta, MD5sum: 0ce84c872fc0072a885926823dcd0338) reference is equivalent to b37, with the exception that it does not contain the decoy sequence for human herpesvirus 4 type 1 (named NC 007605_). This reference grew out of the 1000 Genomes Project. For details see the comparison table.
