dan - 2020-07-27

Are we going to get the latest (patch 13) version of RefSeq GRCh38? If not, is there an easy way to build that reference myself for snpEff? I need consistency in my pipelines that are using RefSeq p13 hg38

UPDATE: I realized I was editing the wrong config file. This message will come up if the genome you're trying to build is not listed in the config file as per the snpEff docs

Still would be nice to have a buit in refSeq GRCh38 patch 13 though

in the default snpEff.config, the p7 FTP url points here: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/
I believe this actually contains to the p13 patch of NCBI's data, indicated by the GCF accession IDs present in the FTP directory (haven't verified this)

GCF_000001405.25_refseqgene_alignments.gff3
GCF_000001405.26_refseqgene_alignments.gff3
GCF_000001405.28_refseqgene_alignments.gff3

But when I try to simply copy the lines over in snpEff.config from p7 refseq to p13 it still won't build the reference

##### GRCh38 current release from NCBI's RefSeq should be p13 not p7 
GRCh38.p13.RefSeq.genome : Human genome GRCh38 using RefSeq transcripts
GRCh38.p13.RefSeq.reference : ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/
        GRCh38.p13.RefSeq.M.codonTable : Vertebrate_Mitochondrial
        GRCh38.p13.RefSeq.MT.codonTable : Vertebrate_Mitochondrial

 snpEff download -v GRCh38.p13.RefSeq
00:00:00    SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00    Command: 'download'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p13.RefSeq'
00:00:00    Reading config file: /var/www/html/ordium/pub/snpEff.config
00:00:00    Reading config file: /usr/local/bin/snpEff/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.p13.RefSeq.genome' not found
    at org.snpeff.interval.Genome.<init>(Genome.java:106)
    at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
    at org.snpeff.snpEffect.Config.init(Config.java:480)
    at org.snpeff.snpEffect.Config.<init>(Config.java:117)
    at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)

Thanks

 

Last edit: dan 2020-07-28