MC values and phasing information

[ireneadm]

Hi
I am lloking at the VCF file from your dataset page m21009_241011_231051.GRCh38.trgt.sorted.phased.vcf.gz
and I am a bit confused on the order of the MC values when we have phasing information, for example

chr6 16327633 . GTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGATGCTGATGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC GTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGATGCTGATGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 0 . TRID=ATXN1;END=16327723;MOTIFS=TGC;STRUC=(TGC)n GT:AL:ALLR:SD:MC:MS:AP:AM:PS 1|0:90,93:90-91,90-93:9,7:30,31:0(0-90),0(0-93):0.977778,0.978495:.,.:15906760

is the MC 30 referring the number of repeats of the alternative allele or the order is in case of heterozygosity is always MC REF, ALT?

Thanks a lot for your help!

[egor-dolzhenko]

Thank you for the question! Yes, unfortunately, phasing modifies the GT field in TRGT VCFs but leaves the other fields unchanged. TRGT will always report the lower allele index first so 1|0 was originally 0/1 (similarly 2|1 was 1/2). I hope this helps!

[ireneadm]

Thank you for the answer. Does this mean that for 1|0, the MC is anyway reporting the repeat count for the lower allele first? thanks again!

[egor-dolzhenko]

Of course! In this case, yes. In general, TRGT will report the repeat count for the reference allele first (regardless if it is shorter or longer than the other allele).