When looking at the credible set qualityControls flags, it's odd that credible sets from SuSiE-inf have the flag Study locus finemapped without in-sample LD reference but not the PICS credible sets.
In [25]: cs.filter(f.col("studyType") == "gwas").groupBy("finemappingMethod", "qualityControls").count().show(truncate = False)
+-----------------+---------------------------------------------------------------------------------------------------------------------------------------+------+
|finemappingMethod|qualityControls |count |
+-----------------+---------------------------------------------------------------------------------------------------------------------------------------+------+
|SuSie |[Study locus with a sum of PIPs that not in the expected range [0.99,1]] |14804 |
|pics |[Study locus from curated top hit, Variant not found in LD reference, Study has quality control flag(s)] |3029 |
|pics |[] |24535 |
|pics |[Study locus from curated top hit, Study has quality control flag(s)] |131146|
|pics |[Study has quality control flag(s)] |20385 |
|pics |[Variant not found in LD reference, Study has quality control flag(s)] |1604 |
|SuSie |[] |2698 |
|pics |[Variant not found in LD reference] |5549 |
|pics |[LD block does not contain variants at the required R^2 threshold, Study has quality control flag(s)] |315 |
|SuSiE-inf |[Study locus finemapped without in-sample LD reference] |261318|
|pics |[LD block does not contain variants at the required R^2 threshold] |6510 |
|pics |[Study locus from curated top hit, LD block does not contain variants at the required R^2 threshold, Study has quality control flag(s)]|3620 |
+-----------------+---------------------------------------------------------------------------------------------------------------------------------------+------+
Adding the OUT_OF_SAMPLE_LD quality control flag would be good when computing PICS credible sets.
When looking at the credible set
qualityControlsflags, it's odd that credible sets fromSuSiE-infhave the flagStudy locus finemapped without in-sample LD referencebut not the PICS credible sets.Adding the
OUT_OF_SAMPLE_LDquality control flag would be good when computing PICS credible sets.