Read my VCF file with an error.

[Xiao-Zhong]

Hi Andrew,

I just started using antigen.garnish for a VCF file I have, but it reported the error below that I cannot overcome.

> garnish_variants("test.vcf") Loading VCFs Scanning file to determine attributes. File attributes: meta lines: 531 header_line: 532 variant count: 2 column count: 11 Meta line 531 read in. All meta lines processed. gt matrix initialized. Character matrix gt created. Character matrix gt rows: 2 Character matrix gt cols: 11 skip: 0 nrows: 2 row_num: 0 Processed variant: 2 All variants processed Error in vdt[, INFO %>% unique()] %>% is.na() || !vdt[, INFO %>% stringr::str_detect(stringr::fixed("ANN=")) %>% : 'length = 2' in coercion to 'logical(1)'

The VCF file is like below, and whole file is attached also. Please help me fix the issue! Thank you very much!

test2.vcf.txt

##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 | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##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 NORMAL TUMOR
chr1 17538 . C A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=31,42|5,8;DP=89;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=233,189;MMQ=43,33;MPOS=46;NALOD=1.36;NLOD=6.62;POPAF=6;TLOD=26.1;ANN=A|upstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|transcript|ENST00000619216.1|miRNA||n.-102G>T|||||102|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328.2|processed_transcript||n.*3129C>A|||||3129|,A|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305.2|transcribed_unprocessed_pseudogene||n.*3868C>A|||||3868|,A|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147.1|unprocessed_pseudogene|5/10|n.574+68G>T|||||| GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:29,0:0.042:29:9,0:11,0:22,0:12,17,0,0 0/1:44,13:0.209:57:20,3:12,4:33,8:19,25,5,8
chr1 1299290 . C A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=44,50|2,2;DP=98;ECNT=1;GERMQ=93;MBQ=20,20;MFRL=177,252;MMQ=60,60;MPOS=22;NALOD=1.46;NLOD=8.43;POPAF=6;TLOD=5.51;ANN=A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000467278.5|retained_intron||n.-335G>T|||||335|,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000470659.1|retained_intron||n.-4282G>T|||||4282|,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000379037.6|processed_transcript||n.-1025G>T|||||1025|,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000493992.1|retained_intron||n.-1049G>T|||||1049|,A|upstream_gene_variant|MODIFIER|MIR6726|ENSG00000278073|transcript|ENST00000613751.1|miRNA||n.-3120G>T|||||3120|,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000478065.5|retained_intron||n.*2158G>T|||||2158|,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000479108.5|retained_intron||n.*2566G>T|||||2566|,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000438966.1|processed_transcript||n.*3920G>T|||||3920|,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000354980.7|nonsense_mediated_decay||n.*1323G>T|||||906|,A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000354700.10|protein_coding|10/23|c.750+55G>T||||||,A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000492936.5|retained_intron|9/21|n.2489+55G>T||||||,A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000353662.4|protein_coding|8/20|c.624+55G>T||||||,A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000476572.1|retained_intron|1/5|n.273+55G>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000472541.5|retained_intron|9/9|n.1400G>T|||||| GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:41,0:0.033:41:9,0:17,0:28,0:18,23,0,0 0/1:53,4:0.081:57:12,0:20,2:33,2:26,27,2,2

[Xiao-Zhong]

Andrew's reply in another Issues may be helpful here as well:
Please use the docker container.
Posted here just want to save anyone who will also encounter the issue.