bcftools | official development repository for BCFtools

by samtools C Version: 1.17 License: Non-SPDX

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kandi X-RAY | bcftools Summary

bcftools is a C library. bcftools has no bugs, it has no vulnerabilities and it has low support. However bcftools has a Non-SPDX License. You can download it from GitHub.

This is the official development repository for BCFtools. It contains all the vcf* commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools. For a full documentation, see bcftools GitHub page.

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Quality

Security

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Support

bcftools has a low active ecosystem.

It has 530 star(s) with 220 fork(s). There are 47 watchers for this library.

It had no major release in the last 12 months.

There are 237 open issues and 1409 have been closed. On average issues are closed in 50 days. There are 8 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of bcftools is 1.17

Quality

bcftools has 0 bugs and 0 code smells.

Security

bcftools has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

bcftools code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

bcftools has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

bcftools releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

It has 5483 lines of code, 27 functions and 5 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

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bcftools Key Features

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bcftools Examples and Code Snippets

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Community Discussions

Trending Discussions on bcftools

How to run a bash script inside a snakemake pipeline

Snakemake: MissingInputException - Missing input files for rule all

Keep getting error: [E::fai_build3_core] Failed to open the file --regions for a script I have been using

Snakemake integrate the multiple command lines in a rule

Replace 2nd and 3rd occurrence of a character with another character, for each line, Bash

Snakemake on cluster error: 'Wildcards' object has no attribute 'output'

Dependencies plot-vcfstats in conda environment

nextflow: change part of the script basing on a parameter

Output format of bcftools view

Bash script using gzip and bcftools running out of memory with large files

QUESTION

How to run a bash script inside a snakemake pipeline

Asked 2022-Mar-31 at 13:13

I would like to run a bash script inside the snakemake pipeline. But I do not know how to call the input and output of snakemake in a bash script.

snakemake:

...

ANSWER

Answered 2022-Mar-31 at 13:13

You need to get the input arguments using bash syntax, snakemake@input[0] is specifically for R scripts using a script directive.

In particular, you can replace snakemake@input[0] with $1, which gets the first argument to a bash script and snakemake@output[0] with $2, the second argugment. To be safe, wrap those with double quotes in case there are spaces in the filenames, e.g. "$1".

Source https://stackoverflow.com/questions/71689090

QUESTION

Snakemake: MissingInputException - Missing input files for rule all

Asked 2022-Feb-28 at 19:44

I am trying to make a snakemake workflow for whatshap haplotype caller but I am struggling with MissingInputException errors. This is what I get:

...

ANSWER

Answered 2022-Feb-26 at 01:06

Troy Comi has already answered your question in comments, but I will explain it further.

Indeed, removing double braces will help. The difference between single and double braces is that double braces escape the symbol '{' and '}'. In other words whenever Snakemake encounters a string like this one "{{sample}}/{sample}_phased_illumina_FILT5.vcf.gz" in the output section, it treats {sample} as a wildcard and {{sample}} as a string "{sample}". So it tries to find the files like {sample}/saturna_phased_illumina_FILT5.vcf.gz which it definitely fails to find.

The problem is quite different in case of using this string in the expand function:

Source https://stackoverflow.com/questions/71249606

QUESTION

Keep getting error: [E::fai_build3_core] Failed to open the file --regions for a script I have been using

Asked 2022-Feb-25 at 19:45

I have been using the below script however, I keep getting an error on the output. Any ideas why?

...

ANSWER

Answered 2022-Feb-25 at 19:45

Suggesting to replace line:

Source https://stackoverflow.com/questions/71266991

QUESTION

Snakemake integrate the multiple command lines in a rule

Asked 2022-Feb-07 at 04:30

The output of my first command line "bcftools query -l {input.invcf} | head -n 1" prints the name of the first individual of vcf file (i.e. IND1). I want to use that output in selectvariants GATK in -sn IND1 option. How is it possible to integrate the 1st comamnd line in snakemake in order to use it's output in the next one?

...

ANSWER

Answered 2022-Feb-04 at 12:52

I think I found a solution:

Source https://stackoverflow.com/questions/70985443

QUESTION

Replace 2nd and 3rd occurrence of a character with another character, for each line, Bash

Asked 2022-Feb-03 at 04:28

I am trying to reformat the reference legend files to make them compatible with bcftools.

Essentially, I need to go from this:

...

ANSWER

Answered 2022-Feb-03 at 04:28

If sed is an option:

Source https://stackoverflow.com/questions/70965847

QUESTION

Snakemake on cluster error: 'Wildcards' object has no attribute 'output'

Asked 2022-Jan-11 at 14:29

I'm running into an error of 'Wildcards' object has no attribute 'output', similar to this earlier question 'Wildcards' object has no attribute 'output', when I submit Snakemake to my cluster. I'm wondering if you have any suggestions for how to make this compatible with the cluster?

While my rule annotate_snps works when I test it locally, I get the following error on the cluster:

...

ANSWER

Answered 2022-Jan-11 at 14:29

The raw rule definition appears to be consistent except for the multiple calls to the contents of config, e.g. config[snpeff].

One thing to check is if the config definition on the single machine and on the cluster is the same, if it's not there might be some content that is confusing snakemake, e.g. if somehow config[snpeff] == "wildcards.output" (or something similar).

Source https://stackoverflow.com/questions/70615842

QUESTION

Dependencies plot-vcfstats in conda environment

Asked 2021-Oct-22 at 04:24

I have a conda environment where I have packages including bcftools installed. I am using bcftools stats to generate some stats on my VCF files. Then, I want to plot the generated stats using plot-vcfstats, also from bcftools. However, this command turned out to be dependent on certain packages that didn't install when I installed bcftools in my conda env. The output I got when running plot-vcfstats:

...

ANSWER

Answered 2021-Oct-22 at 04:24

Seems like a mess. Some of the comments in this open issue imply that Conda's texlive-core is broken, but not really clear there is an authoritative response there.

On osx-64 platform, I can get semi-functionality with the environment:

Source https://stackoverflow.com/questions/69659849

QUESTION

nextflow: change part of the script basing on a parameter

Asked 2021-Jul-20 at 02:58

I have a Nextflow workflow that's like this (reduced):

...

ANSWER

Answered 2021-Jul-20 at 02:58

The general pattern is to use a local variable in the 'script' block and a ternary operator to add the -f PASS,. filter option when params.filter_pass is true:

Source https://stackoverflow.com/questions/68442177

QUESTION

Output format of bcftools view

Asked 2021-Mar-09 at 16:45

I am using Bcftools to extract a single sample VCF from a GVCF file.

...

ANSWER

Answered 2021-Mar-09 at 16:45

You can also try

Source https://stackoverflow.com/questions/66472946

QUESTION

Bash script using gzip and bcftools running out of memory with large files

Asked 2021-Jan-21 at 23:11

This bash script is meant to be part of a pipeline that processes zipped .vcf file that contain genomes from multiple patients (which means the files are huge even when zipped, like 3-5GB).

My problem is that I keep running out of memory when running this script. It is being run in a GCP high mem VM.

I am hoping there is a way to optimize the memory usage so that this doesn't fail. I looked into it but found nothing.

...

ANSWER

Answered 2021-Jan-21 at 23:11

If you run out of memory when using bcftools query/view or gzip look for options in the manual that might reduce the memory footprint. In case of gzip you might also switch to an alternative implementation. You could even consider switching the compression algorithm altogether (zstd is pretty good).

However, I have a feeling that the problem could be for line in `cat ${base}_list.txt`;. The whole file ..._list.txt is loaded into memory before the loop even starts. Also, reading lines that way has all kinds of problems, like splitting lines at whitespace, expanding globs like * and so on. Use this instead:

Source https://stackoverflow.com/questions/65836117

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