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Tools to work with GWAS-VCF summary statistics files
The `+munge` plugin appears to fail to read the last column of a tab-delimited header line if it starts with a `#` character. So the following (tab-delimited, b37 positions) issued...
Dear Guilio: I downloaded the **1kg_ldgm**.*.**bcf** files for **AFR, EAS, EUR, HIS, SAS**. Now let's say that I have **a SNP list file including 100 SNPs** within a LD block....
It seems impossible to install using the instructions as written. There is no makefile provided, so the required make call just won't ever work. Is there an easier way to...
Hi, I'm working on comparative genomics across divergent species. For each species/population, I map the sequencing data to their own reference genome, do variant calling, and apply statistical phasing to...
Thanks for making such a useful tool! I have discovered one unusual edge case where it doesn't seem to work right. In VEGFC, there is a 3bp deletion in hg38...
Hi, Thank you again for this great set of tools ! In the interest of promoting the adoption of gwas-vcf and my first time experience with your plugins (very fast...
I am trying to liftover the 1000 genome **genotype likelihood** files. These files contain no genotype data (e.g. no GT field). Instead, they contain the genotype likelihood (e.g. GL Field)....
Hello, I am trying to run liftover on a moderate size (500K PacBio-derived SVs) to lift data from the macaque genome to GRCh37. I am running the command below, but...
When runing a liftover+ from 37 to 38, a warning is displayed for each variant (N=17697744/). If I ignore the warnings and let it continue, the liftover runs to completion...
Hi, I am new to using bcftools +liftover, I want to liftOver from hg38 to hg19. However, I get the error: "Error: the reference allele GT does not match the...
