Liftover¶
The Liftover report builder converts genomic coordinates for variants or genes in a gor file from one build of the human genome to another build.
Liftover module in Sequence Miner¶
Example use case¶
The user wishes to convert a list of genes or variants with coordinates from hg19 to coordinates from hg38.
Description of the algorithm¶
The Liftover query matches genomic coordinates from one build to another build.
Interpreting the output¶
Genomic coordinates that correspond to the desired build are returned where available.
Column descriptions¶
Group |
Column |
Description |
|---|---|---|
Basic |
Call |
The actual called sequence (variant), found by replacing a part of the reference sequence, denoted by POS and Reference, with the sequence in the Call column |
CHROM |
The chromosome of the variant, represented as chr1, chr2, …, chr22, chrXY, chrX, chrY, chrM |
|
POS |
The (first) base pair position of the sequence variant, e.g., the position of the first nucleotide in the Reference column |
|
Reference |
Sequence from the reference build, the first base starting at the base pair position in the POS column |
|
hg19 |
CHROM |
The chromosome of the variant, represented as chr1, chr2, …, chr22, chrXY, chrX, chrY, chrM |
liftoverStatus |
Mapped if liftover was successful |
|
POS |
The (first) base pair position of the sequence variant, e.g., the position of the first nucleotide in the Reference column |
|
qStrand |
“+” or “-” |