Latest version for GRCm38 ( release 102 )

[Just08]

Hi,
I would like to get a database for GRCm38.102. I've tried to do it myself with "snpEff.jar build" because the pipeline for which I want this version use SnpEff4.3t but for protein check step I have only "." character.

My command :

wget -nv http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz \
mkdir -p ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102 \
mv Mus_musculus.GRCm38.102.gtf.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/genes.gtf.gz \
wget -nv http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz \
mv Mus_musculus.GRCm38.pep.all.fa.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/protein.fa.gz \
wget -nv http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz \
mv Mus_musculus.GRCm38.cdna.all.fa.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/cds.fa.gz \
wget -nv http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz \
mv Mus_musculus.GRCm38.dna.toplevel.fa.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/sequences.fa.gz \
gunzip ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/*.gz \
mkdir ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/regulation.bed \
wget -nv -r -np -nd -A "*.bed.gz" -e robots=off  http://ftp.ensembl.org/pub/release-102/regulation/mus_musculus/Peaks/ \
ls *.bed.gz | awk -F"." -v mvCmd='mv "%s" "%s"\n' '{printf mvCmd,$0,"regulation."$3"."$4".bed.gz"}' | sh \
mv regulation.*.bed.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/regulation.bed/ \
gunzip ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/regulation.bed/*.bed.gz \
curl -H 'Accept: text/pfm' -X GET "https://jaspar.genereg.net/api/v1/species/10090/?version=1&release=2022&page=1&page_size=1000&collection=CORE" > pfm_all_mouse.txt \
gzip -c pfm_all_mouse.txt > ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/pwms.bin \
wget -nv http://ftp.ensembl.org/pub/release-102/regulation/mus_musculus/MotifFeatures/Mus_musculus.GRCm38.motif_features.gff.gz \
mv Mus_musculus.GRCm38.motif_features.gff.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/motif.gff.gz \
gunzip ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/motif.gff.gz \
echo 'GRCm38.102.genome : Mus_musculus' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
echo 'GRCm38.102.reference : ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
java -Xmx20g -jar ${PACKAGE_DIR}/snpEff-4.3T/snpEff.jar build -gtf22 -v GRCm38.102 2>&1 | tee ${PACKAGE_DIR}/snpEff-4.3T/GRCm38.102.build

I have the same issue that were reported here for the regulation part : #304 (comment)

I have 0 motif load :

[Optional] Reading motifs: GFF
#51 1605.7 00:02:30             Loading PWMs from : /opt/snpEff-4.3T/./data/GRCm38.102/pwms.bin
#51 1605.7 00:02:30             Loading motifs from : /opt/snpEff-4.3T/./data/GRCm38.102/motif.gff
#51 1633.2 00:02:58             Loadded motifs: 0
#51 1633.2 00:02:58             Saving motifs to: /opt/snpEff-4.3T/./data/GRCm38.102/motif.bin

Database requests :

Organism name: Mus_musculus
Link gene definition file (e.g. GTF / GFF / GenBank): http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz
Link to Genome FASTA file/s
: http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz
Link to CDS FASTA file: http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Link to Protein FASTA file: http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz
Regulation : http://ftp.ensembl.org/pub/release-102/regulation/mus_musculus/Peaks/
Motif : http://ftp.ensembl.org/pub/release-102/regulation/mus_musculus/MotifFeatures/Mus_musculus.GRCm38.motif_features.gff.gz
Jaspar = https://jaspar.genereg.net/api/v1/species/10090/?version=1&release=2022&page=1&page_size=1000&collection=CORE

Thanks in advance for your help.

[pcingola]

Closing old issues. GRCm39.105 has been added for SnpEFF VERSION 5.1