MungeSumstats

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liftover not working for certain region

1

## 1. Bug description I am running liftover over a series of LD blocks. It works fine for all chromosomes until chromosome 17, and then after I reach one LD...

zhana-optima

Large number of non-biallelic SNPs

14

I'm munging a bunch of OpenGWAS data with MSS, and i noticed that the number of variants dropped due to being non-biallelic was quite high (hundreds of thousands-millions). In some...

bschilder

Option to specify effect allele as A1 instead.

13

Can an option be added to the main function to consider A1 as the effect allele instead? I have attempted to this manually, but it is inelegant without manipulating scripts...

svenkatesh25

dbSNP154

1

I am using MungSumstats package to standardize GWAS catalog data. MungSumstats uses dbSNP155 whereas at present GWAS Catalog uses dbSNP154, I wanted to ask how MungSumstats handles this issue? Many...

AhmedArslan

Fix GitHub Action

8

https://github.com/neurogenomics/MungeSumstats/actions/runs/6652926537/job/18077848264 It seems the`rworkflows` GHA is failing due to the inability get some some resource files: ``` The downloaded binary packages are in /var/folders/3s/vfzpb5r51gs6y328rmlgzm7c0000gn/T//RtmpokJdJw/downloaded_packages ── R CMD build ───────────────────────────────────────────────────────────────── *...

bschilder

Finding manual of previous versions

4

Hi Al, Thanks again for the awesome tool! I was wondering if there is any way to access the manual for a previous version of MSS? I have recently updated...

jksull

SNPlocs.Hsapiens.dbSNP156.GRCh37

4

Hi, how can I access to the SNPlocs.Hsapiens.dbSNP156.GRCh37 or SNPlocs.Hsapiens.dbSNP156.GRCh38. Thank you!

AndyYang0924

Join results in more than 2^31 rows for format_sumstats

3

## 1. Bug description Hi! I run this code to standardize the summary statistics: ``` data = fread('C:/Folder/trait_qc.sumstats.csv.gz') reformatted C:\Users\P70~1\AppData\Local\Temp\RtmpQNDQJX\file371020c95a84.tsv.gz Standardising column headers. First line of summary statistics file: SNP...

Snigireva

Extend quality control and standardisation to QTL analysis

2

Extend quality control and standardisation to QTL analysis. Following checks are specific to QTL studies and need to be added: * Allow for duplicated SNPs * Check effect region/gene region...

Al-Murphy

`cannot find an open port. For manually specifying the port, see ?SnowParamUsing previously downloaded VCF.`

1

## 1. Bug description `import_sumstats`: Works fine for 100s of GWAS, then encounters this error and quickly iterates through all remaining GWAS ids without actually processing them (and, strangely, appends...

bschilder