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.