Using SnpSift to filter VCF for protein_coding regions not working

Question

[goatsrunfaster]

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(VcfFileIterator.java:216) at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:57) at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123) at org.snpsift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:351) at org.snpsift.SnpSiftCmdFilter.run(SnpSiftCmdFilter.java:331) at org.snpsift.SnpSift.run(SnpSift.java:588) at org.snpsift.SnpSift.main(SnpSift.java:76)

Any help is appreciated.

[Pierre Lindenbaum]

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

[goatsrunfaster]

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?

[goatsrunfaster]

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

-Spencer