Is there an official documentation about the differences between hg38 and GRCh38?
To my understanding, there is no differences between them.
However, in gnomAD, which uses GRCh38, SNVs are in the following format: 19-44908822-C-T, without the chr prefix https://gnomad.broadinstitute.org/variant/19-44908822-C-T. Sometimes there is even a discrepancy within the same VCF file, for instance in the high coverage 1000 Genomes dataset (https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/ , where the chromosome names are chr1, whereas the ID is without chr (for instance 22:10519265:CA:C).
1 answer
To my understanding, there is no differences between them.
Primary genome sequence should be identical. There is more in this thread --> Difference between the Fasta files from UCSC and Gencode/Ensembl
UCSC's FAQ page has several questions that would be of interest: https://genome.ucsc.edu/FAQ/FAQgenes.html
Broad's GRCh38 sequences are available from their resource bundle: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle
Log in to answer this question.
-
Why is NA18498 sample missing from 1000 genome GRCh38 vcf file?
written by octpus616 •
-
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
written by octpus616 •
-
Which 1000 genomes 30x files should I use for imputation?
written by Apprentice
-
"SNP" record in vcf looks like this: 6:28035427:GTA:ATA ?
written by curious
-
Using 1000 genomes phase 3 variants for BQSR
written by prasundutta87
-
1000 genomes missing SNPs on chr X in GRCh38
written by b_ha •
-
1000 Human Genomes Project Population Alignment Data
written by AXR •
-
differences between Illumina Platinum Variant Calls and NIST variant calls
written by kspata
-
Mate mismatch errors in 1000genomes CRAM files
written by Mehulsharma.253 •
-
News: 1000 Genomes data on GRCh38
written by fairley •
