I have 10 normal/tumor samples and I did the following:-
1. Generated vcfs
2. Normalised them
3. Merged together
Now I want to annotate the merged vcf, using java -Xmx4g -jar snpEff.jar -v -stats ex1.html GRCm38.75 finalMerge.vcf > final.anno.vcf
but I am getting an error
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: 'GRCm38.75'
00:00:00 Reading config file: /media/shayantanbanerjee/disk1/20_cancer_samples/dfata/snpEff/snpEff.config
00:00:00 done
00:00:00 Reading database for genome version 'GRCm38.75' from file '/media/shayantanbanerjee/disk1/20_cancer_samples/dfata/snpEff/./data/GRCm38.75/snpEffectPredictor.bin' (this might take a while)
00:00:09 done
00:00:09 Loading Motifs and PWMs
00:00:09 Building interval forest
00:00:12 done.
00:00:12 Genome stats :
#-----------------------------------------------
# Genome name : 'Mus_musculus'
# Genome version : 'GRCm38.75'
# Genome ID : 'GRCm38.75[0]'
# Has protein coding info : true
# Has Tr. Support Level info : true
# Genes : 39179
# Protein coding genes : 23232
#-----------------------------------------------
# Transcripts : 94929
# Avg. transcripts per gene : 2.42
# TSL transcripts : 0
#-----------------------------------------------
# Checked transcripts :
# AA sequences : 52148 ( 99.75% )
# DNA sequences : 82932 ( 87.36% )
#-----------------------------------------------
# Protein coding transcripts : 52278
# Length errors : 4872 ( 9.32% )
# STOP codons in CDS errors : 40 ( 0.08% )
# START codon errors : 4814 ( 9.21% )
# STOP codon warnings : 3254 ( 6.22% )
# UTR sequences : 48094 ( 50.66% )
# Total Errors : 8962 ( 17.14% )
#-----------------------------------------------
# Cds : 432486
# Exons : 628052
# Exons with sequence : 628052
# Exons without sequence : 0
# Avg. exons per transcript : 6.62
# WARNING! : Mitochondrion chromosome 'MT' does not have a mitochondrion codon table (codon table = 'Standard'). You should update the config file.
#-----------------------------------------------
# Number of chromosomes : 80
# Chromosomes : Format 'chromo_name size codon_table'
# '1' 195471971 Standard
# '2' 182113224 Standard
# 'MG4214_PATCH' 171031749 Standard
# 'X' 171031299 Standard
# '3' 160039680 Standard
# '4' 156508116 Standard
# 'MG4136_PATCH' 156508116 Standard
# 'MG4212_PATCH' 151862668 Standard
# '5' 151834684 Standard
# '6' 149736546 Standard
# '7' 145441459 Standard
# 'MG4151_PATCH' 145439975 Standard
# '10' 130694993 Standard
# '8' 129401213 Standard
# '14' 124902244 Standard
# '9' 124595110 Standard
# 'MG132_PATCH' 124595110 Standard
# '11' 122082543 Standard
# 'MG3829_PATCH' 122082543 Standard
# '13' 120421639 Standard
# 'MG4180_PATCH' 120129530 Standard
# '12' 120129022 Standard
# '15' 104043685 Standard
# 'MG3833_PATCH' 98208653 Standard
# '16' 98207768 Standard
# '17' 94987271 Standard
# 'MG4222_MG3908_PATCH' 94987243 Standard
# 'MG4211_PATCH' 91797447 Standard
# 'MG4209_PATCH' 91793962 Standard
# 'Y' 91744698 Standard
# 'MG4213_PATCH' 91736668 Standard
# 'MG3835_PATCH' 90835696 Standard
# '18' 90702639 Standard
# '19' 61431566 Standard
# 'MG153_PATCH' 61431565 Standard
# 'JH584299.1' 953012 Standard
# 'GL456233.1' 336933 Standard
# 'JH584301.1' 259875 Standard
# 'GL456211.1' 241735 Standard
# 'GL456350.1' 227966 Standard
# 'JH584293.1' 207968 Standard
# 'GL456221.1' 206961 Standard
# 'JH584297.1' 205776 Standard
# 'JH584296.1' 199368 Standard
# 'GL456354.1' 195993 Standard
# 'JH584294.1' 191905 Standard
# 'JH584298.1' 184189 Standard
# 'JH584300.1' 182347 Standard
# 'GL456219.1' 175968 Standard
# 'GL456210.1' 169725 Standard
# 'JH584303.1' 158099 Standard
# 'JH584302.1' 155838 Standard
# 'GL456212.1' 153618 Standard
# 'JH584304.1' 114452 Standard
# 'GL456379.1' 72385 Standard
# 'GL456216.1' 66673 Standard
# 'GL456393.1' 55711 Standard
# 'GL456366.1' 47073 Standard
# 'GL456367.1' 42057 Standard
# 'GL456239.1' 40056 Standard
# 'GL456213.1' 39340 Standard
# 'GL456383.1' 38659 Standard
# 'GL456385.1' 35240 Standard
# 'GL456360.1' 31704 Standard
# 'GL456378.1' 31602 Standard
# 'GL456389.1' 28772 Standard
# 'GL456372.1' 28664 Standard
# 'GL456370.1' 26764 Standard
# 'GL456381.1' 25871 Standard
# 'GL456387.1' 24685 Standard
# 'GL456390.1' 24668 Standard
# 'GL456394.1' 24323 Standard
# 'GL456392.1' 23629 Standard
# 'GL456382.1' 23158 Standard
# 'GL456359.1' 22974 Standard
# 'GL456396.1' 21240 Standard
# 'GL456368.1' 20208 Standard
# 'MT' 16299 Standard
# 'JH584292.1' 14945 Standard
# 'JH584295.1' 1976 Standard
#-----------------------------------------------
00:00:14 Predicting variants
VcfFileIterator.parseVcfLine(132): Fatal error reading file 'finalMerge.vcf' (line: 1):
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java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
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at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:133)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:184)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:57)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:467)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:142)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1029)
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)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
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at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1007)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:219)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:130)
... 9 more
00:00:14 Logging
00:00:15 Checking for updates...
00:00:16 Done.
Hello,
please post the first lines of you finalMerge.vcf. It looks like it isn't a real vcf file. It looks like there is something binary in it (bcf??)
fin swimmer
Thanks for replying. The first lines of the vcf file are illegible too. Something like this \8B\00\00\00\00\00\FF\00BC\00\D04͝
The command used to merge the vcfs was:
bcftools merge -Ob -m -any s1.vcf.gz s2.vcf.gz ..... > merge.vcf