Question: Using SnpSift to filter VCF for protein_coding regions not working
0
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(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.

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!

-Spencer

ADD REPLYlink written 7 months ago by goatsrunfaster20
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: 1140 users visited in the last hour