No white-space, semi-colons, or equals-signs are permitted in INFO field values

[rrdavis77]

Hi,

I am trying to annotate some VCF files with some COSMIC data (latest realeve V91) but the INFO filed for the COSMIC vcf has "=" in it and snpsift throws this error:

java.lang.RuntimeException: No white-space, semi-colons, or equals-signs are permitted in INFO field values. Name:"AA" Value:"p.W263R,p.W344R,p.W235R,p.W343R,p.L211P,p.W218R,p.L116P,p.P288=,p.W281R"

I am on version 4.3T

SnpSift version 4.3t (build 2017-11-24 10:18), by Pablo Cingolani

Here is the header of the COSMIC vcf:

`ryan@ubuntu:~/NGS/$ head -n 20 CosmicCodingMuts.vcf

fileformat=VCFv4.1

source=COSMICv91

reference=GRCh38

fileDate=20200324

comment="Missing nucleotide details indicate ambiguity during curation process"

comment="URL stub for ID field (use the whole COSV identifier)='https://cancer.sanger.ac.uk/cosmic/search?genome=38&q='"

comment="REF and ALT sequences are both forward strand

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

CHROM POS ID REF ALT QUAL FILTER INFO

1 65797 COSV58737189 T C . . GENE=OR4F5_ENST00000641515;STRAND=+;LEGACY_ID=COSN23957695;SNP;CDS=c.9+224T>C;AA=p.?;HGVSC=ENST00000641515.2:c.9+224T>C;HGVSG=1:g.65797T>C;CNT=1`

Thanks for any help you can provide!

Ryan