dbSnp_annotate nasty bug

[drosofff]

I don't know yet where report this bug properly because I could determine whether the issue comes from the tool, the Galaxy wrapper, or the dbsnp VCF - or an interaction between these possibilities.

In any case:

With galaxy wrapper snpSift_annotate (Galaxy Version 4.3+t.galaxy1)

• when selecting ID field + INFO fields
• with dbsnp156 vcf

##fileDate=20221104
##source=dbSNP
##dbSNP_BUILD_ID=156
##reference=GRCh38.p14

• requesting for the field CLNHGVS cause failure on the tool and missing lines in the
  VCF output.

the stderror of the tool is

Picked up _JAVA_OPTIONS: -Xms512m
java.lang.RuntimeException: No white-space, semi-colons, or equals-signs are permitted in INFO field values. Name:"CLNHGVS" Value:"NC_000001.11:g.156114934=,NC_000001.11:g.156114934C>T"
	at org.snpeff.vcf.VcfEntry.addInfo(VcfEntry.java:263)
	at org.snpsift.annotate.AnnotateVcfDb.annotateInfo(AnnotateVcfDb.java:161)
	at org.snpsift.annotate.AnnotateVcfDb.annotate(AnnotateVcfDb.java:105)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:128)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:90)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:410)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:397)
	at org.snpsift.SnpSift.run(SnpSift.java:588)
	at org.snpsift.SnpSift.main(SnpSift.java:76)
java.lang.RuntimeException: No white-space, semi-colons, or equals-signs are permitted in INFO field values. Name:"CLNHGVS" Value:"NC_000001.11:g.156115584=,NC_000001.11:g.156115584T>A,NC_000001.11:g.156115584T>C,NC_000001.11:g.156115584T>G"
	at org.snpeff.vcf.VcfEntry.addInfo(VcfEntry.java:263)
	at org.snpsift.annotate.AnnotateVcfDb.annotateInfo(AnnotateVcfDb.java:161)
	at org.snpsift.annotate.AnnotateVcfDb.annotate(AnnotateVcfDb.java:105)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:128)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:90)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:410)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:397)
	at org.snpsift.SnpSift.run(SnpSift.java:588)
	at org.snpsift.SnpSift.main(SnpSift.java:76)
java.lang.RuntimeException: No white-space, semi-colons, or equals-signs are permitted in INFO field values. Name:"CLNHGVS" Value:"NC_000001.11:g.156135626=,NC_000001.11:g.156135626A>G"
	at org.snpeff.vcf.VcfEntry.addInfo(VcfEntry.java:263)
	at org.snpsift.annotate.AnnotateVcfDb.annotateInfo(AnnotateVcfDb.java:161)
	at org.snpsift.annotate.AnnotateVcfDb.annotate(AnnotateVcfDb.java:105)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:128)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:90)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:410)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:397)
	at org.snpsift.SnpSift.run(SnpSift.java:588)
	at org.snpsift.SnpSift.main(SnpSift.java:76)
java.lang.RuntimeException: No white-space, semi-colons, or equals-signs are permitted in INFO field values. Name:"CLNHGVS" Value:"NC_000001.11:g.156137375=,NC_000001.11:g.156137375A>G"
	at org.snpeff.vcf.VcfEntry.addInfo(VcfEntry.java:263)
	at org.snpsift.annotate.AnnotateVcfDb.annotateInfo(AnnotateVcfDb.java:161)
	at org.snpsift.annotate.AnnotateVcfDb.annotate(AnnotateVcfDb.java:105)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:128)
	at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:90)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:410)
	at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:397)
	at org.snpsift.SnpSift.run(SnpSift.java:588)
	at org.snpsift.SnpSift.main(SnpSift.java:76)

Tests

• COMMON,FREQ,GNO,PSEUDOGENEINFO,CLNDISDB,GENEINFO,INT,CLNSIG,dbSNPBuildID,NSF,R3,R5,NSN,NSM,CLNORIGIN,RS,ASS # success

• COMMON,FREQ,GNO,PSEUDOGENEINFO,CLNDISDB,GENEINFO,INT,CLNSIG,dbSNPBuildID,NSF,R3,R5,NSN,NSM,CLNORIGIN,RS,ASS,U3,U5,CLNACC,CLNDN,DSS # success

• COMMON,FREQ,GNO,PSEUDOGENEINFO,CLNDISDB,GENEINFO,INT,CLNSIG,dbSNPBuildID,NSF,R3,R5,NSN,NSM,CLNORIGIN,RS,ASS,U3,U5,CLNACC,CLNDN,DSS,SYN,CLNVI,VC,SAO # success

• COMMON,FREQ,GNO,PSEUDOGENEINFO,CLNDISDB,GENEINFO,INT,CLNSIG,dbSNPBuildID,NSF,R3,R5,NSN,NSM,CLNORIGIN,RS,ASS,U3,U5,CLNACC,CLNDN,DSS,SYN,CLNVI,VC,SAO,PUB,CLNHGVS,PM # failure

valid fields (success)

COMMON,FREQ,GNO,PSEUDOGENEINFO,CLNDISDB,GENEINFO,INT,CLNSIG,dbSNPBuildID,NSF,R3,R5,NSN,NSM,CLNORIGIN,RS,ASS,U3,U5,CLNACC,CLNDN,DSS,SYN,CLNVI,VC,SAO,PUB,PM

invalid field

CLNHGVS