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frazer-lab / i2QTL-SV-STR-analysis

Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as part of the i2QTL consortium. This data set consists of sequencing data from the iPSCORE (Frazer lab) and HipSci projects.
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LD information of between SVs/STRs and SNPs #1

Open Lee211 opened 5 years ago

Lee211 commented 5 years ago

This is a great work! I want to know whether you can provide the LD information of between SVs/STRs and SNPs? or provide all SVs/STRs/SNPs at the individual level?

djakubosky commented 5 years ago

Thanks for your kind words, the maximum LD between each SV/STR with a variant within 50kb included in the UKBB in the non-redundant call set (MAF 5%) is currently available in my second manuscript describing eQTLs from these data. At a later date I may also be making available the strongest LD between the SV/STRs and any nearby SNV or indel called in our i2QTL WGS data (gatk).

see manuscript 2 supplemental table 4. i2QTL SV/STR eQTLs

I am in the process of uploading all of the variants (including those that don't pass QC) to DBGap as an annotated VCF file (with information about clusters of redundant variants etc). This will include genotypes for all individuals if you have access to the dbGAP.

Also, be on the lookout for a second repo I am making public shortly containing the analyses from this second manuscript, as well as additional updates to this repo.