675bc34c80612e44b7a251390d6567611f92a37e max Thu Dec 8 03:03:47 2022 -0800 fixing grc incidents - liftover related links, refs #30355 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index e594a16..f3eda3b 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -1,42 +1,39 @@ # A space delimited file of track relatedness, format: # ucscDb track trackLinkingTo reason # hg38: hg38 miRnaAtlas nonCodingRNAs View associated precursor miRnas hg38 nonCodingRNAs miRnaAtlas View expression of cleaved miRnas hg38 caddSuper gnomad View associated variants hg38 gnomad caddSuper View CADD scores for this variant and region hg38 revel liftHg38 Revel is based on hg19 and lifted to hg38. liftOver "chain" alignment from hg19 to hg38 hg38 liftHg38 revel Revel scores were lifted using UCSC liftOver chains from hg38 hg38 revel caddSuper CADD, a similar deleteriousness score, and not used as an input by REVEL hg38 caddSuper revel REVEL, a similar deleteriousness score -hg38 liftOverHg38 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed -hg38 grcIncidentDb liftOverHg38 LiftOver for hg38, explores how incident regions aligned between human assemblies - -hg38 grcIncidentDb liftOverHg19 LiftOver alignments between hg19 and hg38, to explore how the GRC incident assembly changes affect whole-genome alignments between hg19 and hg38 used for lifting data from hg19 -hg38 liftOverHg19 grcIncidentDb GRC IncidentDb shows version issues, to explore alignment between human assemblies +hg38 liftHg19 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed +hg38 grcIncidentDb liftHg19 LiftOver for hg38, explores how incident regions aligned between human assemblies # hg19: hg19 caddSuper gnomad View associated variants hg19 gnomad caddSuper View CADD scores for this variant and region hg19 decipherHaploIns gnomadPLI Compare haploinsufficiency metrics as defined by gnomAD hg19 gnomadPLI decipherHaploIns Compare constraint metrics as defined by DECIPHER hg19 revel caddSuper CADD, a similar deleteriousness score, and not used as an input by REVEL hg19 caddSuper revel REVEL, a similar deleteriousness score -hg19 liftOverHg38 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed -hg19 grcIncidentDb liftOverHg38 LiftOver alignments between hg38 and hg38 to explore how the GRC incident assembly changes affect whole-genome alignments between hg19 and hg38 used for lifting data from hg19 +hg19 liftHg38 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed +hg19 grcIncidentDb liftHg38 LiftOver alignments between hg38 and hg38 to explore how the GRC incident assembly changes affect whole-genome alignments between hg19 and hg38 used for lifting data from hg19 -hg19 fixSeqLiftOverPsl liftOverHg38 Investigate how patches affect the whole-genome alignment used for liftOver -hg19 liftOverHg38 fixSeqLiftOverPsl Investigate how assembly patches affect the liftOver alignment +hg19 fixSeqLiftOverPsl liftHg38 Investigate how patches affect the whole-genome alignment used for liftOver +hg19 liftHg38 fixSeqLiftOverPsl Investigate how assembly patches affect the liftOver alignment -hg19 liftOverHg38 hg38ContigDiff Hg38 Diff shows contigs that were changed from hg19 to hg38 -hg19 hg38ContigDiff liftOverHg38 Investigate how contig changes affect the liftOver alignments +hg19 liftHg38 hg38ContigDiff Hg38 Diff shows contigs that were changed from hg19 to hg38 +hg19 hg38ContigDiff liftHg38 Investigate how contig changes affect the liftOver alignments