<STR0> vs NA in ExpansionHunter VCF output files

[roel1289]

Hello,

I have a quick question regarding the notation of ExpansionHunter VCF output files.

Occasionally, I will have results that show repeat unit counts for both alleles:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CTRL-NEUXY894VJR-03876-G_1.final
chr5    109340618       .       C       <STR1>,<STR14>  .       PASS    END=109340679;REF=8;RL=61;RU=GGGGAGA;VARID=PJA2;REPID=PJA2      GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC     1/2:SPANNING/FLANKING:1/14:0-1/10-44:1/0:2/5:0/0:39.162162

while other times, the results show repeat counts for two alleles, but one of them is a 0:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CASE-NEUBL463FP2-01331-G_1.final
chr5    109340618       .       C       <STR0>,<STR85>  .       PASS    END=109340679;REF=10;RL=61;RU=GGGAGA;VARID=PJA2;REPID=PJA2      GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC     1/2:SPANNING/INREPEAT:0/85:0-0/24-291:1/0:0/1:0/3:49.326122

and finally, sometimes, the results just show counts for one allele:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  CASE-NEUAE431CGV-02066-G_1.final
chr5    109340618       .       C       <STR15> .       PASS    END=109340679;REF=10;RL=61;RU=GGGAGA;VARID=PJA2;REPID=PJA2      GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC     1/1:FLANKING/FLANKING:15/15:7-15/13-322:0/0:2/2:0/0:35.034613

I am wondering what the difference is between <STR0> and just having no alleles at all.

Thanks!
Ross

[andreasssh]

Both the first and second example there are 2 different alleles which differ from the reference (genotypes 1/14 and 0/85). On the third example you have one allele in homozygous state (genotype 15/15), so the only alternate non-reference allele (ALT) that is present is 15 which is shown there as STR15.