Hi, I am trying to understand these Manta somatic variant VCFs that I have annotated with VEP.
chr10 11974892 MantaBND:6118:0:1:0:0:0:0 G ]chr1:41850074]G . PASS SVTYPE=BND;MATEID=MantaBND:6118:0:1:0:0:0:1;CIPOS=0,2;HOMLEN=2;HOMSEQ=AG;SOMATIC;SOMATICSCORE=54;BND_DEPTH=62;MATE_BND_DEPTH=0;CHR2=chr1;ENDPOSSV=41850074;SVLEN=0;RO=-+;TRA;LENSV=-1;RGENUPS=ENSCAFG00000045430___None,-9947,+;RGENISEC=ENSCAFG00000000435___BEST3,0,-;RGENDNS=ENSCAFG00000000436___RAB3IP,59491,+;LGENUPS=ENSCAFG00000000405___PLEKHG1,-146330,+;LGENISEC=ENSCAFG00000000413___MTHFD1L,0,+;LGENDNS=ENSCAFG00000000419___AKAP12,173336,+;CSQ=]chr1:41850074]G|feature_truncation|HIGH|MTHFD1L|MTHFD1L_3|Transcript|XM_038526323.1|mRNA||||||||||||1||||Canis_familiaris.UU_Cfam_GSD_1.0.gtf.gz|,]chr1:41850074]G|feature_truncation&intron_variant|HIGH|BEST3|BEST3_2|Transcript|XM_038549568.1|mRNA||4/5||||||||||-1||||Canis_familiaris.UU_Cfam_GSD_1.0.gtf.gz| PR:SR:RDISTDISC1:RDISTDISC2:RCDIS1:RCDIS2:RUT1:RUT2:DRNOISE1:DRNOISE2:CLMQ1:CLMQ2:EVALRCNOISE 7,0:25,0:0:0:0:0:1:1:0,0,0,0,0,0:0,0,0,0,0,0:0,0,186:0,0,2:1,1 9,0:29,16:0:0:0:0:1:1:0,0,0,0,3,3:0,0,0,0,15,15:0,0,487:0,0,41:0,0
I have consulted the manual https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md#vcf-info-fields
but cannot seem to find information regarding these fields; "RGENISEC" ,"RGENDNS", "LGENUPS","LGENISEC". Additionally I see "RGENUPS" "LGENDNS". After each of these appears what seems to be a different gene, for example after LGENUPS: ENSCAFG00000000405___PLEKHG1 would be PLEKHG1. However the location of the first column chr10:11974892 belongs to a unannotated region and the alternative allele MTHF1L. So I am not sure what gene to attribute this variant to. Additionally I noticed that the reference that for many of these the SVLEN field is 0 meaning there is no difference in length between the reference and alternate alleles. I do not quite understand what the entry is telling me in that case. My initial thought was "A break point was found at chromosome 10 pos 11974892 that was inserted at chr1 pos 41850074" so this would be a translocation. However, again I am not sure what part of what gene was translocated where?
It is also possible I am completely incorrect and if anybody could help it would be much appreciated. Thanks
it must be defined in the VCF header.