# Merge vcfs like bcftools merge **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [April 3, 2020, 5:37pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361 "2020-04-03T17:37:57Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [April 3, 2020, 5:37pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361/1 "2020-04-03T17:37:57Z")
Hi there, I’m wondering if there is a best practice for merging VCFs together in hail, akin to the `bcftools merge` function. Best Nick ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [April 3, 2020, 6:12pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361/2 "2020-04-03T18:12:34Z")
What kind of merge? Inner/outer on variants, samples, etc? ---
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [April 3, 2020, 7:45pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361/3 "2020-04-03T19:45:23Z")
Sorry about not having enough info. I have 50k sample vcfs, and I want to merge them into single vcf keeping all variants found in any sample (outer). ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [April 3, 2020, 7:55pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361/4 "2020-04-03T19:55:26Z")
Are these GVCFs or VCFs? If the former, there’s a good solution. The latter, it’s going to be very difficult/impossible to get a sensible result, partly because VCFs are lossy (no reference blocks) ---
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [April 3, 2020, 8:04pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361/5 "2020-04-03T20:04:39Z")
It’s the latter. I’m okay with a bunch of no calls in the merged VCF with all the samples because these are somatic variant calls, and I don’t expect any variant to be common. If that was your concern. Or is there another concern I’m not catching? ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [April 3, 2020, 8:14pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361/6 "2020-04-03T20:14:51Z")
this is a duplicate of: > [@Outer Joining Multiple VCFs](https://discuss.hail.is/t/outer-joining-multiple-vcfs/1350): > > Hello! I wanted to see if there’s a simple way to outer join multiple VCFs in Hail. I have ~50,000 VCFs each of which has somatic calls from 1 individual, and basically my goal is to perform QC on each VCF (ex: removing non-PASS variants and low-qual genotypes), then join all the 50,000 VCFs into 1 hail .mt (I don’t need any entry-level info on each variant except for GT and VAF, VEP-annotate that .mt, and export\_entries on for downstream analysis. Would be fantastic if there was a way to do t… This is possible to do by writing a hierarchical merge with intermediate checkpoints, but it’ll probably take an hour or two to write down the correct code for that and I don’t have time right now. ---
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [April 3, 2020, 8:32pm UTC](https://discuss.hail.is/t/merge-vcfs-like-bcftools-merge/1361/7 "2020-04-03T20:32:16Z")
Oh thats funny. Alright. I’ll try writing something up. Thanks!