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I'm trying to get CSV files from snpEff -csvStats option and got stuck. I tried the code below and only got the vcf file with no contents. How can I use -csvStats option properly?

snpEff -Xmx4g -csvStats -v hg19 08_FILTER/NA12878.Filtered.Variants.vcf > test.ann.vcf

    00:00:00  SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
    00:00:00  Command: 'ann'
    00:00:00  Reading configuration file 'snpEff.config'. Genome: '08_FILTER/NA12878.Filtered.Variants.vcf'
    00:00:00  Reading config file: /home/ubuntu/01_NA12878/snpEff.config
    00:00:00  Reading config file: /home/ubuntu/miniconda2/share/snpeff-4.3.1t-2/snpEff.config
    java.lang.RuntimeException: Property: '08_FILTER/NA12878.Filtered.Variants.vcf.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.SnpEffCmdEff.run(SnpEffCmdEff.java:1000)
      at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
      at org.snpeff.SnpEff.run(SnpEff.java:1183)
      at org.snpeff.SnpEff.main(SnpEff.java:162)
    00:00:00  Logging

00:00:01  Done.

 snpEff -Xmx4g -v hg19 -csvStats 08_FILTER/NA12878.Filtered.Variants.vcf > tes2.ann.vcf

00:00:25  Genome stats :
#-----------------------------------------------
# Genome name                : 'Homo_sapiens (USCS)'
# Genome version             : 'hg19'
# Genome ID                  : 'hg19[0]'
#     'M' 16571   Vertebrate_Mitochondrial
#     'Un_gl000226'   15008   Standard
#     '18_gl000207_random'    4262    Standard
#     'MT'    1   Vertebrate_Mitochondrial
#-----------------------------------------------

00:00:27  Predicting variants

Here is the snpEff.config file. I installed the snpEff at /miniconda2/share .

# Databases are stored here
# E.g.: Information for 'hg19' is stored in data.dir/hg19/
#
# You can use tilde ('~') as first character to refer to your home directory. 
# Also, a non-absolute path will be relative to config's file dir
# 
#---
data.dir = ./data/

#---
# Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName')
#---
database.repository = http://downloads.sourceforge.net/project/snpeff/databases

#---
# Latest version numbers. Check here if there is an update.
#---
versions.url = http://snpeff.sourceforge.net/versions.txt

#-------------------------------------------------------------------------------
# Third party databases
#-------------------------------------------------------------------------------

# Databases for human GRCh38 (hg38)

database.clinvar.GRCh38                 = ./db/GRCh38/clinvar/clinvar-latest.vcf.gz
database.repository.clinvar             = ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar-latest.vcf.gz

database.dbsnp.GRCh38                   = ./db/GRCh38/dbSnp/dbSnp.vcf.gz
database.repository.dbsnp.GRCH38        = ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz

database.dbnsfp.GRCH38                  = ./db/GRCh38/dbNSFP/dbNSFP.txt.gz

# Databases for human GRCh37 (hg19)
database.clinvar.GRCh37                 = ./db/GRCh37/clinvar/clinvar-latest.vcf.gz
database.repository.clinvar.GRCh37      = ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar-latest.vcf.gz

database.dbsnp.GRCh37                   = ./db/GRCh37/dbSnp/
database.repository.dbsnp.GRCh37        = ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b141_GRCh37p13/VCF/

database.gwascatalog.GRCh37             = ./db/GRCh37/gwasCatalog/gwascatalog.txt
database.repository.gwascatalog.GRCh37  = http://www.genome.gov/admin/gwascatalog.txt

database.dbnsfp.GRCh37                  = ./db/GRCh37/dbNSFP/dbNSFP.txt.gz

#-------------------------------------------------------------------------------
# Loss of function (LOF) 
#-------------------------------------------------------------------------------

# It is assumed that even with a protein coding change at the 
# last 5% of the protein, the protein could still be functional.
lof.ignoreProteinCodingAfter  : 0.95

#  It is assumed that even with a protein coding change at the 
#  first 5% of the protein: 
#       "..suggesting some disrupted transcripts are 
#       rescued by transcriptional reinitiation at an 
#       alternative start codon."
lof.ignoreProteinCodingBefore : 0.05

# Larger deletions removing either the first exon or more than 
# 50% of the protein-coding sequence of the affected transcript
lof.deleteProteinCodingBases : 0.50

#-------------------------------------------------------------------------------
# Codon tables
#
# Format:   It's a comma separated "codon/aminoAcid[+*]" list 
#           Where 'codon' is in uppper case, aminoAcid is a one letter 
#           code, '+' denotes start codon and '*' denotes stop codon.
#
# References:   http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
#               ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt
#-------------------------------------------------------------------------------
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  • $\begingroup$ Hmmmm. The message Genome: '08_FILTER/NA12878.Filtered.Variants.vcf' is confusing me. That's not in this snpEff.config file. Is it in the other config file? The terminal output includes /home/ubuntu/01_NA12878/snpEff.config and /home/ubuntu/miniconda2/share/snpeff-4.3.1t-2/snpEff.config. If the VCF file isn't in either config file, my next guess would be that the command-line arguments are declared incorrectly. I don't know enough about snpEff to troubleshoot that without more context, though. :( $\endgroup$ Jul 30 '19 at 14:34
  • $\begingroup$ @DanielStandage I've got the one more issue with the installation, I thought it might be something with snpEff installed in miniconda2, so I deleted the snpEff and re-installed it in the prior directory of it, I realized it's not a good idea so I removed the snpEff again and installed the snpEff at /share/miniconda2 again. And now I'm getting error snpEff: command not found, how can I make this working? $\endgroup$
    – kwoo
    Jul 30 '19 at 15:41
  • $\begingroup$ @DanielStandage I mean, how can I make just 'snpEff' code working without java jar? It worked before I re-installed it but now I think something is twisted. I don't have an idea cause snpEff -Xmx4g -v hg19 08_FILTER/${sample}.Filtered.Variants.vcf > 09_ANN/${sample}.ann.vcf worked without -csvStats option well. $\endgroup$
    – kwoo
    Jul 30 '19 at 16:02
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Had the same issue, but found that I need to provide a filename to use the csvstats option

snpEff -Xmx4g -csvStats stats.csv -v hg19 08_FILTER/NA12878.Filtered.Variants.vcf > test.ann.vcf
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