Question: SnpSift annotate outputs invalid files?
0
gravatar for B
4.9 years ago by
B0
B0 wrote:

Hey, I'm fairly new to all of this, so sorry in advance if I miss something that should be obvious. I am trying to annotate some VCF files with information from various databases. All of the input files seem valid because they don't raise any flags when I check them with SnpSift's vcfcheck. But I can't seem to run the output files through anything, and when I run the output files through vcfcheck, I get this error:


VcfFileIterator.parseVcfLine(114):      Fatal error reading file 'GE_annotated.vcf' (line: 1):
??# # f i l e f o r m a t = V C F v 4 . 0

Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).

??# # f i l e f o r m a t = V C F v 4 . 0

        at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:115)
        at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:166)
        at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:56)
        at ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:84)
        at ca.mcgill.mcb.pcingola.fileIterator.MarkerFileIterator.hasNext(MarkerFileIterator.java:62)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdVcfCheck.check(SnpSiftCmdVcfCheck.java:36)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdVcfCheck.run(SnpSiftCmdVcfCheck.java:57)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:335)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:70)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).

??# # f i l e f o r m a t = V C F v 4 . 0

        at ca.mcgill.mcb.pcingola.vcf.VcfEntry.parse(VcfEntry.java:850)
        at ca.mcgill.mcb.pcingola.vcf.VcfEntry.<init>(VcfEntry.java:124)
        at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:112)
        ... 8 more


I have gotten the similar errors using different vcf's and different databases (so I doubt that a particular input file is causing the problem). I made sure to double-check the number of columns, and it seems to be correct, so I am not sure what is wrong. The line it is complaining about is also in the input file, so I don't know why it seems to be causing an error now. I'm not sure if the semicolons that SnpSift put into the file to separate different entries in the same column might be causing problems, or if there's something else going on. Any help would be much appreciated.

vcf snpeff snpsift software error • 2.0k views
ADD COMMENTlink modified 4.1 years ago by talushm0 • written 4.9 years ago by B0

Are you sure it accepts VCF version 4.0? This format seems pretty outdated.

ADD REPLYlink written 4.9 years ago by mkulecka320

I don't know. I am having trouble finding documentation for more recent formats beyond 4.2. Would the files from 1000 Genomes be outdated?

ADD REPLYlink written 4.9 years ago by B0
0
gravatar for talushm
4.1 years ago by
talushm0
United States
talushm0 wrote:

Had the same issue. Just index the database if it's bgzipped.

ADD COMMENTlink written 4.1 years ago by talushm0
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: 1677 users visited in the last hour