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Hello,
I'm working on benchmarking some tandem repeat genotypers and I was looking for the well-known pathogenic CAG HTT repeat in the adotto_TRregions_v1.2.bed BED file.
However, there doesn't seem to be an entry for the CAG repeat in the BED file. Is this just because it doesn't vary from HG38 in HG002?
The text was updated successfully, but these errors were encountered:
The region we have documented for HTT from our Patho.csv is at
chr4
3074876
3074966
HTT
CAG
This intersects in the adotto_TRregions_v1.2:
chr4
3074938
3075085
Which is included as a tier1 region in the GIAB TR v1.0
chr4
3074938
3075085
Tier1
TN_TN_TN
14
0.7933
-4
0
28
So there perhaps is a discrepancy in the boundaries between the catalog and the patho.csv by 62bp which may be messing up your query region's overlap to the catalog?
However, I was expecting to see the CAG repeat as an entry in the anno column of the BED file, since it's the best-known expansion location and motif for HTT repeat variation, with the GCC coming after.
My goal is to produce a BED file with motifs to feed to various STR genotypers, so extracting this chr4:3074938-3075048 region from hg38 gives a more heterogeneous repeat then what I would expect (and is missing a repeat I'd like to have), which would be two STR entries: CAG in chr4:3074877-3074940, and GCC in ~chr4:3074941-3075052.
Hello,
I'm working on benchmarking some tandem repeat genotypers and I was looking for the well-known pathogenic CAG HTT repeat in the
adotto_TRregions_v1.2.bed
BED file.However, there doesn't seem to be an entry for the CAG repeat in the BED file. Is this just because it doesn't vary from HG38 in HG002?
The text was updated successfully, but these errors were encountered: