Which GRCh37 version to use from snpEff databases for BAMs mapped with GRCh37-lite?

Question

[CHANG]

Does anyone know which version of GRCh37 to use from snpEff databases to annotate VCF files generated from BAMS mapped with GRCh37-lite.

(https://browser.cghub.ucsc.edu/help/assemblies/)

GRCh37-lite

• This is a subset of the full GRCh37 human genome assembly (assembly accession GCA_000001405.1) plus the human mitochondrial genome reference sequence (the "rCRS") from Mitomap.org. This set of sequences excludes all the alternate loci scaffolds of the full GRCh37 assembly, and has the pseudo-autosomal regions (PARs) on chromosome Y masked with Ns. This haploid representation of the genome is provided as a convenience for use in alignment pipelines that cannot handle the multiple placements expected in the PARs and in regions of the genome that are represented by the alternate loci. The assembly is available at ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/.

snpEff databases

java -jar snpEff.jar databases | grep -i sapiens

GRCh37.64    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.64.zip
GRCh37.65    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.65.zip
GRCh37.66    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.66.zip
GRCh37.68    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.68.zip
GRCh37.69    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.69.zip
GRCh37.70    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.70.zip
GRCh37.71    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.71.zip
GRCh37.72    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.72.zip
GRCh37.73    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.73.zip
GRCh37.74    Homo_sapiens     http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_GRCh37.74.zip
GRCh37.75    Homo_sapiens

Answer 1

[Pablo]

GRCh37.XX are form ENSEMBL genes. I'd recommend you use the latest one available (GRCh37.75).