Dear all, i am using SnpEff to annotate my VCF file but i see some error
i use hg19 of Snpeff database ( i didn't build) to annotate my vcf file
here is the result
java -Xmx10g -jar snpEff.jar eff -c snpEff.config -v hg19 accepted_hits-snp-dbsnp.vcf > accepted_hits-snp-dbsnp-eff.vcf
00:00:00.000 Reading configuration file '../../../../../tools/snpeff_snpsift/snpEff/snpEff.config'. Genome: 'hg19'
00:00:00.302 done
00:00:00.302 Reading database for genome version 'hg19' from file '/home/huypham/tools/snpeff_snpsift/snpEff/./data/hg19/snpEffectPredictor.bin' (this might take a while)
00:00:07.050 done
00:00:07.081 Building interval forest
00:00:15.896 done.
00:00:15.896 Genome stats :
# Genome name : 'Homo_sapiens (USCS)'
# Genome version : 'hg19'
# Has protein coding info : true
# Genes : 26346
# Protein coding genes : 20775
# Transcripts : 47313
# Avg. transcripts per gene : 1.80
# Protein coding transcripts : 38612
# Length errors : 210 ( 0.54% )
# STOP codons in CDS errors : 193 ( 0.50% )
# START codon errors : 14 ( 0.04% )
# STOP codon warnings : 0 ( 0.00% )
# Total Errors : 239 ( 0.62% )
# Cds : 388149
# Exons : 459403
# Exons with sequence : 459403
# Exons without sequence : 0
# Avg. exons per transcript : 9.71
# Number of chromosomes : 93
# Chromosomes names [sizes] :
...
NEW VERSION!
There is a new SnpEff version available:
Version : 3.6
Release date : 2014-04-21
Download URL : http://sourceforge.net/projects/snpe...atest_core.zip
how can i explain about the error which i bold?
thank you.
i use hg19 of Snpeff database ( i didn't build) to annotate my vcf file
here is the result
java -Xmx10g -jar snpEff.jar eff -c snpEff.config -v hg19 accepted_hits-snp-dbsnp.vcf > accepted_hits-snp-dbsnp-eff.vcf
00:00:00.000 Reading configuration file '../../../../../tools/snpeff_snpsift/snpEff/snpEff.config'. Genome: 'hg19'
00:00:00.302 done
00:00:00.302 Reading database for genome version 'hg19' from file '/home/huypham/tools/snpeff_snpsift/snpEff/./data/hg19/snpEffectPredictor.bin' (this might take a while)
00:00:07.050 done
00:00:07.081 Building interval forest
00:00:15.896 done.
00:00:15.896 Genome stats :
# Genome name : 'Homo_sapiens (USCS)'
# Genome version : 'hg19'
# Has protein coding info : true
# Genes : 26346
# Protein coding genes : 20775
# Transcripts : 47313
# Avg. transcripts per gene : 1.80
# Protein coding transcripts : 38612
# Length errors : 210 ( 0.54% )
# STOP codons in CDS errors : 193 ( 0.50% )
# START codon errors : 14 ( 0.04% )
# STOP codon warnings : 0 ( 0.00% )
# Total Errors : 239 ( 0.62% )
# Cds : 388149
# Exons : 459403
# Exons with sequence : 459403
# Exons without sequence : 0
# Avg. exons per transcript : 9.71
# Number of chromosomes : 93
# Chromosomes names [sizes] :
...
NEW VERSION!
There is a new SnpEff version available:
Version : 3.6
Release date : 2014-04-21
Download URL : http://sourceforge.net/projects/snpe...atest_core.zip
how can i explain about the error which i bold?
thank you.
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