|
Post by Albert on Aug 29, 2020 3:18:40 GMT
Hi I'm using SMR for meQTL and eQTL, and it stuck at 0% when start checking the consistency of alleles.
Options: --bfile LD/1000G.EUR.QC_bfile --beqtl-summary QTL_binary/meQTL_smr --beqtl-summary QTL_binary/cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense --out SMR/SMR_me2e
Reading eQTL SNP information from [QTL_binary/cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense.esi]. 8932843 SNPs to be included from [QTL_binary/cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense.esi]. Reading eQTL probe information from [QTL_binary/cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense.epi]. 19250 Probes to be included from [QTL_binary/cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense.epi]. Reading eQTL summary data from [QTL_binary/cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense.besd]. eQTL summary data of 19250 Probes to be included from [QTL_binary/cis-eQTLs-full_eQTLGen_AF_incl_nr_formatted_20191212.new.txt_besd-dense.besd]. Reading eQTL SNP information from [QTL_binary/meQTL_smr.esi]. 4447326 SNPs to be included from [QTL_binary/meQTL_smr.esi]. Reading PLINK FAM file from [LD/1000G.EUR.QC_bfile.fam]. 489 individuals to be included from [LD/1000G.EUR.QC_bfile.fam]. Reading PLINK BIM file from [LD/1000G.EUR.QC_bfile.bim]. 9997231 SNPs to be included from [LD/1000G.EUR.QC_bfile.bim]. Checking the consistency of the alleles of each SNP between pairwise data sets (including the GWAS summary data, the eQTL summary data and the LD reference data).
0%
Could someone help? Thank you!
|
|
ax
New Member
Posts: 27
|
Post by ax on Dec 24, 2020 2:31:47 GMT
It is likely that those three data sets have very different allele frequency. Sometimes it is because your input format has some issues.
|
|
|
Post by Wendy Hipple on Jan 18, 2023 20:01:18 GMT
To the freeforums.net Owner, similar here: <a href="http://695example695.com" rel="nofollow">Link Text</a>
|
|
|
Post by XXXXX on Jan 19, 2023 15:14:38 GMT
Hi freeforums.net Webmaster, very same listed here: <a href="http://695example695.com" rel="nofollow">Link Text</a>
|
|