Question: Using SnpSift to filter VCF for protein_coding regions not working
gravatar for goatsrunfaster
7 months ago by
goatsrunfaster20 wrote:

I have annotated a VCF file using snpEff which has worked wonderfully. Now I am trying to filter that file based on protein-coding regions but just get an outfile file with nothing in it, and the error below:

java -Xmx4g -jar /network/rit/home/sb939359/turnerlab/bin/snpEff/SnpSift.jar filter "ANN[*].EFFECT has 'protein_coding'" all_no_outgroups.recode.ann.vcf > codons.vcf

Exception in thread "main" java.lang.RuntimeException: Error reading file 'all_no_outgroups.recode.ann.vcf'. Line ignored: Line (0): 'null' at org.snpeff.fileIterator.VcfFileIterator.readNext( at org.snpeff.fileIterator.VcfFileIterator.readNext( at org.snpeff.fileIterator.FileIterator.hasNext( at at at at org.snpsift.SnpSift.main(

Any help is appreciated.

snp next-gen genome • 156 views
ADD COMMENTlink written 7 months ago by goatsrunfaster20

is it really a vcf file ? can you read it with bcftools view all_no_outgroups.recode.ann.vcf

ADD REPLYlink written 7 months ago by Pierre Lindenbaum129k

Apparently it is not. When I view the file before processing with snpEff using bcftools there is no problem. When I open the new annotated file (which I ran through snpEff) in bcftools I get the message: input/output error.

Note that viewing the .vcf in a text editor they look identical with the exception of the added ANN field.

What is going on here?

ADD REPLYlink written 7 months ago by goatsrunfaster20

This was my fault, the file became corrupt or something. I re-did the original filtering and then SnpSift worked. thanks!


ADD REPLYlink written 7 months ago by goatsrunfaster20
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