Question: snpEff: Fatal error reading file the input VCF files and stop runing
0
gravatar for Shicheng Guo
17 months ago by
Shicheng Guo8.5k
Shicheng Guo8.5k wrote:

Here is the error I met when I use snpEff:

snpEff: Fatal error reading file 'All_samples_Exome_QC.DG5.vcf' (line: 115):    0       0       .       GAAGT   -

Here is the script I run:

java -Xmx4g -jar ~/hpc/tools/snpEff/snpEff.jar GRCh37.75 All_samples_Exome_QC.DG5.vcf > All_samples_Exome_QC.DG.ANN.vcf

Here is what I received from snpEff, Any suggestion? It looks I need clear the data in advance:

VcfFileIterator.parseVcfLine(132):      Fatal error reading file 'All_samples_Exome_QC.DG5.vcf' (line: 115):
0       0       .       GAAGT   -
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '-'
        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: WARNING: Unkown IUB code for SNP '-'
        at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1141)
        at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1016)
        at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:984)
        at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:219)
        at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:130)
        ... 9 more
fetal error snpeff • 747 views
ADD COMMENTlink written 17 months ago by Shicheng Guo8.5k
2
gravatar for finswimmer
17 months ago by
finswimmer14k
Germany
finswimmer14k wrote:

WARNING: Unkown IUB code for SNP '-'

You have a - in the 4th column (ALT) which is not allowed. Missing values have to be . in the vcf file.

Furthermore a chromosome 0 and a position 0 looks also quite strange (but should be allowed) ...

ADD COMMENTlink written 17 months ago by finswimmer14k

Yes. I find it. I don't know why they lable them as '-', rather than '.'

Some other missing SNPs, they label them as "." in the VCF files I received.

ADD REPLYlink written 17 months ago by Shicheng Guo8.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1656 users visited in the last hour