# \#bcftools **URL:** https://help.galaxyproject.org/tag/bcftools/97.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Bcftools convert to vcf skipping all rows](https://help.galaxyproject.org/t/bcftools-convert-to-vcf-skipping-all-rows/17485)
**Author:** [@zhenderson1](https://help.galaxyproject.org/u/zhenderson1)\ **Replies:** 3\ **Last updated:** [February 27, 2026, 6:16pm UTC](https://help.galaxyproject.org/t/bcftools-convert-to-vcf-skipping-all-rows/17485 "2026-02-27T18:16:14Z")
I’m trying to convert an example 23andMe dataset into a vcf file using bcftools, but it skips all four rows every time, and consulting the manual wasn’t much help. Any idea what I’m doing wrong? Here’s the dataset: a… --- ## [problems with vcftools merge command](https://help.galaxyproject.org/t/problems-with-vcftools-merge-command/9734)
**Author:** [@Paola\_Orsini](https://help.galaxyproject.org/u/Paola_Orsini)\ **Replies:** 2\ **Last updated:** [August 9, 2024, 3:49pm UTC](https://help.galaxyproject.org/t/problems-with-vcftools-merge-command/9734 "2024-08-09T15:49:37Z")
Hi all, I’m writing to you for an issue on vcftools merge tool. I’m trying to performe the merge of two vcf files with bcftools merge, and the tool seems to work; however, when open the resulting merged vfc file, I see… --- ## [How can I split a VCF file by chromosome?](https://help.galaxyproject.org/t/how-can-i-split-a-vcf-file-by-chromosome/7373)
**Author:** [@anchor](https://help.galaxyproject.org/u/anchor)\ **Replies:** 1\ **Last updated:** [January 25, 2022, 12:38pm UTC](https://help.galaxyproject.org/t/how-can-i-split-a-vcf-file-by-chromosome/7373 "2022-01-25T12:38:19Z")
I have a VCF file (format = vcf\_bgzip) and I would like to obtain multiple separate VCF files by chromosome. I would appreciate any help into how to achieve this using Galaxy. Here is a sample file: ##fileformat=VCFv4.2… --- ## [bcftools merge - translating settings from command line version to Galaxy](https://help.galaxyproject.org/t/bcftools-merge-translating-settings-from-command-line-version-to-galaxy/6477)
**Author:** [@rt20](https://help.galaxyproject.org/u/rt20)\ **Replies:** 1\ **Last updated:** [June 21, 2022, 9:48am UTC](https://help.galaxyproject.org/t/bcftools-merge-translating-settings-from-command-line-version-to-galaxy/6477 "2022-06-21T09:48:50Z")
Hi- I’m trying to merge several vcf files with bcftools merge using Galaxy. The command line I need to use includes these two lines, and I don’t understand where and how to input plugin fill-AN-AC and filter -i 'SUM(AC)\>1… --- ## [Merging VCF files](https://help.galaxyproject.org/t/merging-vcf-files/3590)
**Author:** [@Pranav\_Menon](https://help.galaxyproject.org/u/Pranav_Menon)\ **Replies:** 2\ **Last updated:** [June 16, 2022, 1:46am UTC](https://help.galaxyproject.org/t/merging-vcf-files/3590 "2022-06-16T01:46:14Z")
Hi, I am hoping someone can give me a tool recommendation for the following task. I have generated multiple vcf files and now I want to combine them into one, while eliminating duplicates (variants present in more than… --- ## [How to transform 23andme and ancestry's data to VCF?](https://help.galaxyproject.org/t/how-to-transform-23andme-and-ancestrys-data-to-vcf/7368)
**Author:** [@anchor](https://help.galaxyproject.org/u/anchor)\ **Replies:** 0\ **Last updated:** [January 21, 2022, 4:08am UTC](https://help.galaxyproject.org/t/how-to-transform-23andme-and-ancestrys-data-to-vcf/7368 "2022-01-21T04:08:27Z")
I have sample files from 23andme and Ancestry. I would like to convert those to VCF. I cannot get bcftools to work with this data. I do not understand the difference between the tabular variant input and the samples file… --- ## [Help with bcftools isec](https://help.galaxyproject.org/t/help-with-bcftools-isec/3585)
**Author:** [@G\_Lab](https://help.galaxyproject.org/u/G_Lab)\ **Replies:** 0\ **Last updated:** [May 5, 2020, 4:56pm UTC](https://help.galaxyproject.org/t/help-with-bcftools-isec/3585 "2020-05-05T16:56:49Z")
Hi, I have 3 VCF files with no overlapping samples but with overlapping variants. I’d like to subset the 3 VCFs to only have the common variants and then merge them to create a large VCF with all the samples from the 3 V… --- ## [bcftools norm realignment](https://help.galaxyproject.org/t/bcftools-norm-realignment/2519)
**Author:** [@roselucia](https://help.galaxyproject.org/u/roselucia)\ **Replies:** 7\ **Last updated:** [November 26, 2019, 3:26pm UTC](https://help.galaxyproject.org/t/bcftools-norm-realignment/2519 "2019-11-26T15:26:19Z")
Hi everyone, I have a question regarding bcftools norm ( bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from m… --- ## [bcftools query - How to handle information with same INTO Tag](https://help.galaxyproject.org/t/bcftools-query-how-to-handle-information-with-same-into-tag/2373)
**Author:** [@roselucia](https://help.galaxyproject.org/u/roselucia)\ **Replies:** 1\ **Last updated:** [October 31, 2019, 7:53am UTC](https://help.galaxyproject.org/t/bcftools-query-how-to-handle-information-with-same-into-tag/2373 "2019-10-31T07:53:46Z")
Hi, I tried out the tool bcftools query and it worked well for rather simple queries. However I am stuck at the point where I would like to only extract the first annotation of the ANN Tag in the Info field. This is wh… --- ## [convert 23and me to vcf](https://help.galaxyproject.org/t/convert-23and-me-to-vcf/378)
**Author:** [@cwray](https://help.galaxyproject.org/u/cwray)\ **Replies:** 3\ **Last updated:** [January 10, 2019, 10:53pm UTC](https://help.galaxyproject.org/t/convert-23and-me-to-vcf/378 "2019-01-10T22:53:59Z")
Trying to convert a 23andme tsv file to vcf using bcftools convert to vcf. Building a lesson for UG class. I get this error: Fatal error: Exit code 255 () –tsv2vcf requires the --samples option python: : Unknown error…