Comments (2)
There's a package called VCF-kit that can convert vcf to tabular format easily:
https://vcf-kit.readthedocs.io/en/latest/vcf2tsv/
Example
vk vcf2tsv wide --print-header spliceai_scores.raw.snv.hg19.vcf.gz > spliceai_scores.raw.snv.hg19.tsv
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Thanks @NathanSkene @bschilder for the suggestion!
We actually did fork ldsc and it can read gwasvcf files directly - https://github.com/explodecomputer/ldsc/
e.g.
./ldsc.py --h2 ieu-a-2.vcf.gz --w-ld-chr eur_w_ld_chr/ --ref-ld-chr eur_w_ld_chr/ --out results
I'll make a pull request to the original LDSC repository to see if they will incorporate these new changes.
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Related Issues (20)
- GTEX eQTL
- bug with ieugwasr_to_coloc
- missing values for coloc
- coloc only use 50 snps
- Error in coloc example
- installing gwasglue without finemapr? HOT 1
- remotes:install_github error HOT 3
- MAF missing in several datasets
- new software suggest
- function gwasvcf_to_coloc small typo bug.
- vcf file error
- challenge from hg19 to hg38 for gwasglue HOT 1
- coloc version 5
- Problem parsing VCF
- problem in gwasvcf::query_gwas
- gwasvcf_to_finemapr error: Input is not detected as bcf or vcf format #40
- ERROR: dependency 'gwasvcf' is not available for package 'gwasglue' HOT 2
- Installation issue HOT 3
- Error in gwasvcf::vcf_to_granges(.) : Not all inherits(vcf, c("ExpandedVCF", "CollapsedVCF")) are TRUE. HOT 1
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