garrettjstevens
commented
5 years ago Do you have a public link to the actual VCF? This snippet looks fine, but maybe I can see something from the VCF itself.
Closed enuggetry closed 5 years ago
garrettjstevens
commented
5 years ago Do you have a public link to the actual VCF? This snippet looks fine, but maybe I can see something from the VCF itself.
enuggetry
commented
5 years ago garrettjstevens
commented
5 years ago The header of the file for that track does not match what you pasted above. The file here:
http://graingenes.org:3000/iwgsc1000/vcf_files/1000-170208_AllChr-IWGSC_WGA_v1_SNPList.ann.HC.vcf.gz
has a header of:
##SnpEffVersion="4.3p (build 2017-06-06 09:55), by Pablo Cingolani"
##SnpEffCmd="SnpEff iwgsc.wga.v1 /group/das/DAS5/EXOME_CAPTURE/ExomeSNPcalls_IWGSC_WGA_v1/170208_AllChr-IWGSC_WGA_v1_SNPList.vcf.gz "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | C
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr1A 22298 scaffold38755_22298 T C 100.0 PASS ANN=C|intergenic_region|MODIFIER|CHR_START-TraesCS1A01G000100|CHR_START-TraesCS1A01G000100|intergenic_region|CHR_START-TraesCS1A01G000100|||n.22298T>C||||||
chr1A 22304 scaffold38755_22304 A G 100.0 PASS ANN=G|intergenic_region|MODIFIER|CHR_START-TraesCS1A01G000100|CHR_START-TraesCS1A01G000100|intergenic_region|CHR_START-TraesCS1A01G000100|||n.22304A>G||||||This is not a valid VCF header because it has a FORMAT column header, but no FORMAT column. Getting rid of the FORMAT at the end of the #CHROM\tPOS\tID... line should make it valid.
Also, VCFs should start with the line
##fileformat=VCFv4.3or whatever version of the VCF spec you're using.
enuggetry
commented
5 years ago ugh, put the wrong file there. Thanks, I'll give it a try.
One of my VCF tracks is getting this error. Any suggestions?
Creating an issue
Header Excerpt: