snpEff: Fatal error reading file the input VCF files and stop runing

Question

[Shicheng Guo]

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

Answer 1

[finswimmer]

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) ...

[Shicheng Guo]

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.