Matthew S Lyon

Thanks for your reply, I would be very grateful to try the new functionality. I have a specific case where the variant caller is unable to find a 20bp deletion...

Thanks Lisle ABRA worked well. See IGV screenshot below. Top pane is ABRA, bottom is original bwa. Could you explain how the amplicon function works please? Are you still using...

see here for CICD https://github.com/MRCIEU/ieugwaspy

Hi Jie Yes you can, see [example](https://mrcieu.github.io/gwas2vcf/downstream/#merge) command. I usually use bcftools but you can also use [GATK/Picard](https://gatk.broadinstitute.org/hc/en-us/articles/360037226612-MergeVcfs-Picard-). If you used gwas2vcf to prepare your VCF files then the alleles/effect...

Hi Jie, Yes, GWAS-VCF is just a suggested standard for using VCF to store summary stats, you could prepare your own and even use different keys/columns but we aim for...

Hi @matteofloris I'm sorry to hear you're having problems. The VCF looks fine. I think the MRCIEU/gwasglue package is parsing the values incorrectly. I have created an [issue](https://github.com/MRCIEU/gwasglue/issues/33).

great suggestion, thanks @darked89. I will add soon

Hi @darked89 Thanks for the feedback. 10 hours does seem slow. It typically take 2-4 hours for densely imputed data (10M variants). How many variants are you mapping? The process...

Thanks @darked89. I will look at implementing [cyvcf2](https://academic.oup.com/bioinformatics/article/33/12/1867/2971439) for reading/writing VCF files which is around 7x faster in the published example. In the meantime, you could speed up the conversion...

Hi @darked89 Should give the same results. I doubt the performance would improve though since the SNP lookup is using tabix rather than reading the whole dbsnp VCF. Do you...