pgscatalog/pgs-harmonizer

A pipeline to format and harmonise Polygenic Score (PGS) Catalog Scoring Files within and between different genome builds.

pgs-harmonizer's Issues

Problem variants?

Some reports:

variants with a valid rsid tags but an "Unknown" source reference tag or “NR” genome_build tag, though it also occurs in some novel variants. For example PGS003753_hmPOS_GRCh38.txt.gz rs147937400 (T>C), which seems to correspond to an original reference of GRCh37 (chr6 29068745), but appears unmapped in the PGS Catalog’s GRCh38 harmonized score file (UCSC reports it mapped to chr6 29100968 in GRCh38)

Related to PGScatalog/pgsc_calc#137

Replace HmVCF with code based on pgscatalog_utils/match_variants

The current code is very slow - using match_variants would be much faster and more consistent with what we're doing in pgsc_calc.

Would use a variant of this script: https://github.com/PGScatalog/pgscatalog_utils/blob/main/pgscatalog_utils/match/match_variants.py

Currently it outputs a csv of all possible matches in the log file (along with which one was best), example:

row_nr	accession	chr_name	chr_position	effect_allele	other_allele	effect_weight	effect_type	ID	REF	ALT	matched_effect_allele	match_type	is_multiallelic	ambiguous	match_flipped	best_match	exclude	duplicate_best_match	duplicate_ID	match_IDs	match_status	dataset
0	PGS000018_hmPOS_GRCh37	1	2245570	G	C	-0.0276009	additive	1:2245570:C:G	C	G	G	altref	false	true	false	true	true	false	false	false	excluded	1000G-chr2
0	PGS000018_hmPOS_GRCh37	1	2245570	G	C	-0.0276009	additive	1:2245570:C:G	C	G	C	refalt_flip	false	true	true	false	true	false	false	false	not_best	1000G-chr2
1	PGS000018_hmPOS_GRCh37	1	22132518	G	A	0.023934	additive	1:22132518:G:A	G	A	G	refalt	false	false	false	true	true	false	false	false	excluded	1000G-chr2
2	PGS000018_hmPOS_GRCh37	1	38386727	G	A	-0.0174935	additive	1:38386727:G:A	G	A	G	refalt	false	false	false	true	true	false	false	false	excluded	1000G-chr2
3	PGS000018_hmPOS_GRCh37	1	55496039	T	C	0.0293005	additive	1:55496039:T:C	T	C	T	refalt	false	false	false	true	true	false	false	false	excluded	1000G-chr2
8	PGS000018_hmPOS_GRCh37	1	110298166	G	C	0.0245969	additive	1:110298166:G:C	G	C	G	refalt	false	true	false	true	true	false	false	false	excluded	1000G-chr2
8	PGS000018_hmPOS_GRCh37	1	110298166	G	C	0.0245969	additive	1:110298166:G:C	G	C	C	altref_flip	false	true	true	false	true	false	false	false	not_best	1000G-chr2
9	PGS000018_hmPOS_GRCh37	1	151762308	G	C	0.0209215	additive	1:151762308:C:G	C	G	G	altref	false	true	false	true	true	false	false	false	excluded	1000G-chr2
9	PGS000018_hmPOS_GRCh37	1	151762308	G	C	0.0209215	additive	1:151762308:C:G	C	G	C	refalt_flip	false	true	true	false	true	false	false	false	not_best	1000G-chr2
10	PGS000018_hmPOS_GRCh37	1	154395946	G	A	-0.0197906	additive	1:154395946:A:G	A	G	G	altref	false	false	false	true	true	false	false	false	excluded	1000G-chr2
28	PGS000018_hmPOS_GRCh37	2	164945044	G	C	0.0213456	additive	2:164945044:G:C	G	C	G	refalt	false	true	false	true	true	false	false	true	excluded	1000G-chr2
28	PGS000018_hmPOS_GRCh37	2	164945044	G	C	0.0213456	additive	2:164945044:G:C	G	C	C	altref_flip	false	true	true	false	true	false	false	true	not_best	1000G-chr2
29	PGS000018_hmPOS_GRCh37	2	202799924	C	T	-0.0226885	additive	2:202799924:T:C	T	C	C	altref	false	false	false	true	false	false	false	true	matched	1000G-chr2
30	PGS000018_hmPOS_GRCh37	2	203829225	A	C	-0.0526925	additive	2:203829225:A:C	A	C	A	refalt	false	false	false	true	false	false	false	true	matched	1000G-chr2

The rows of this file could then be processed into the output of the current HmVCF : e.g. a single row per scoring file variant with information about how it was matched or excluded (harmonisation code)

Incorporate VCF FILTER field

Use variant quality information (PASS/FAIL) to select harmonised variants