brentp
commented
3 years ago I'm not sure what's the problem I did this:
$ vcfanno -lua gff_sv.lua.txt gff_sv.conf.txt portion.vcf.txt > o.vcf
=============================================
vcfanno version 0.3.2 [built with go1.13.1]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 3 sources from 1 files
vcfanno.go:156: falling back to non-bgzip
vcfanno.go:248: annotated 30 variants in 0.03 seconds (1157.7 / second)
(base) brentp@lorax:~/Downloads$ bcftools view o.vcf > /dev/null
[W::vcf_parse] Contig 'PKA1H1_STAND_01' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'PKA1H1_STAND_02' is not defined in the header. (Quick workaround: index the file with tabix.)
(base) brentp@lorax:~/Downloads$ grep CHROM o.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ../../sks047VsPkA1H1/Real50_Sks047VsPkA1H1.Assemblytics_structural_variants.bedyou are pulling fields from the GFF that have spaces that might be causing the problem. If you want to remove those, you can add that to your lua code.
damioresegun
Hi, Following the example here: https://brentp.github.io/vcfanno/examples/gff_sv/gff_sv/; I managed to carry out annotation of my vcf file using a gff file for the same isolate. Conf and lua files used are attached. In the conf file, multiple "names" were added because the gff file identifies genes using different terms based on the sources used within it. Command used was: vcfanno -p 32 -ends -lua gff_sv.lua gff_sv.conf isolatename.vcf > Annotatedisolate.vcf Everything worked well, I saw the annotations present and was about to validate by visualising them on IGV and got an error:
"Error loading /home/doresegu/scratch/private/PublicationAnal/AnnotateVCF/sks047Assem.vcf: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /home/doresegu/scratch/private/PublicationAnal/AnnotateVCF/sks047Assem.vcf"I tried another file and got another error:
"Error loading /home/doresegu/scratch/private/PublicationAnal/AnnotateVCF/sks047ONT.vcf: The provided VCF file is malformed at approximately line number 70: The VCF specification does not allow for whitespace in the INFO field. Offending field value was "PRECISE;SVTYPE=DEL;SVLEN=-47;END=69669;CIPOS=-26,26;CILEN=-9,9;RE=22;RNAMES=e67442f0-666c-4c58-a4dc-2d8a56948018,12e39d4c-e6fa-4aef-97d7-b665468a2d04,28e77da8-681d-4cca-bb7d-7719bac5a260,4e01192e-9864-4415-ac76-21db47b8ec8b,50cb02b2-7936-49d4-8d95-2029319d3642,99a31c50-fbb9-49b3-957b-5e7894d5f5cf,9c3d4539-8700-477b-b42d-0a8beb401751,9e24b0e8-cea9-4d60-9f22-fb57ac762ad6,d1cd70ee-0671-4cb4-b6fd-28c3939377ee,d512485e-6333-4746-b2b6-cf491c20bf11,df31bab4-5db3-4aac-8e9b-29dfa3cb3e19,e1066498-9cde-4932-a5c4-e67249147249,722f10c2-2d0b-4f00-acf3-fac7fc67adf8,82efd438-dab8-4449-b9c5-bcc6b31bca34,f1bf235f-0f7e-427a-bb92-f73733fd3b3d,82c87593-a1b5-4bac-ad78-7d7c5bd9975b,9b3967b2-8ee8-4d61-8c58-d9c3063ff39d,86b137d3-3b5e-4811-913a-14051bf1a8c6,4b3ac4f8-352a-41ff-bff8-c9d9593b059e,c613309d-3df8-4936-826a-95dea6351ca6,83c87a56-bdb3-4ff7-bbfd-0e6b455a60d1,4af1bd20-ae3c-4f52-9738-225b94915840;STRAND=+-;Gene_name=PKA1H1_STAND_CTG000068;protein_match=;polypeptide_product=term%3Dchitinase%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:PKNH_0100800.1,Dbxref=UniProt:Q76EB4,EC:3.2.1.14,Ontology_term=GO:0004553,GO:0005975;left_Gene_name=PKA1H1_STAND_CTG000068;left_protein_match=;left_polypeptide_product=term%3Dchitinase%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:PKNH_0100800.1,Dbxref=UniProt:Q76EB4,EC:3.2.1.14,Ontology_term=GO:0004553,GO:0005975;right_Gene_name=PKA1H1_STAND_CTG000068;right_protein_match=;right_polypeptide_product=term%3Dchitinase%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:PKNH_0100800.1,Dbxref=UniProt:Q76EB4,EC:3.2.1.14,Ontology_term=GO:0004553,GO:0005975", for input source: /home/doresegu/scratch/private/PublicationAnal/AnnotateVCF/sks047ONT.vcf"So I used vcf-validator (from vcftools) to check and I got this type of error: seems like it supports the IGV error for the same isolate
"Broken VCF header, no column names? at /mnt/shared/scratch/doresegu/apps/conda/envs/vcfanno/lib/site_perl/5.26.2/Vcf.pm line 172, <__ANONIO__> line 2. Vcf::throw(Vcf4_1=HASH(0x558de1de9320), "Broken VCF header, no column names?") called at /mnt/shared/scratch/doresegu/apps/conda/envs/vcfanno/lib/site_perl/5.26.2/Vcf.pm line 867 VcfReader::_read_column_names(Vcf4_1=HASH(0x558de1de9320)) called at /mnt/shared/scratch/doresegu/apps/conda/envs/vcfanno/lib/site_perl/5.26.2/Vcf.pm line 602 VcfReader::parse_header(Vcf4_1=HASH(0x558de1de9320)) called at /mnt/shared/scratch/doresegu/apps/conda/envs/vcfanno/lib/site_perl/5.26.2/Vcf.pm line 2557 VcfReader::run_validation(Vcf4_1=HASH(0x558de1de9320)) called at /mnt/shared/scratch/doresegu/apps/conda/envs/vcfanno/bin/vcf-validator line 60 main::do_validation(HASH(0x558de1818220)) called at /mnt/shared/scratch/doresegu/apps/conda/envs/vcfanno/bin/vcf-validator line 14"**I check with the untouched query file and it loaded onto IGV fine. I also attempted to find a vcf fixing tool but can't seem to find anything. Do you have an idea of why the whitespace is being added and why its saying that the CHROM column is missing even though it is present? The header and first 20 lines of the VCF are also attached.
Hopefully I have given you enough to troubleshoot? Please and thanks**
gff_sv.lua.txt gff_sv.conf.txt portion.vcf.txt Cultured_sorted.gff3.gz
If you have encountered an error, please include: