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Questions tagged [bcftools]

BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

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.bcfzip file is imported by software only if recompressed. File content remains the same

I am testing interoperability between two softwares and need a file exported from one to be read by other. The file consists of some xml and jpg files compressed in a .zip format (extensions generated by the programs are .bcf and .bcfzip). As far as…
Luís Filipe Longo
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Output format of bcftools view

I am using Bcftools to extract a single sample VCF from a GVCF file. bcftools view -f -Oz -s Sample_name -o output_sample.vcf.gz input_file.vcf.gz Unfortunately, it seems that the format of the output is not Bgzip compressed, despite the use of…
Drosera_capensis
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How to know whether a unix command execution is successful

I recently tried a bcftools command (to handle variant files) in my command line. The command that I tried is given below bcftools merge --force-samples -O z -o final.vcf.gz ethn.vcf.gz However, the command was working but took a long time to…
The Great
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bcftools make fails with numerous vcfmerge errors in win10

I want to compile latest github bcftools but I get these errors below. [Install instructions]https://raw.githubusercontent.com/samtools/bcftools/develop/INSTALL mentions: git clone git://github.com/samtools/htslib.git git clone…
barnyard
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ALT column of VCF file contains an alternative nucleotide AND <*>

Why does the ALT column of my VCF file sometimes contains an alternative nucleotide as well as a "symbolic allele" <*>? What does it mean? Image of ALT Additionally, in the INFO field, the AD tag tells me that zero reads have the symbolic allele…
Code_Aelita
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Combine shell command lines in snakemake

I would like to combine two command lines as one single to avoid the intermediate files. workdir: "/path/to/workdir/" rule all: input: "my.filtered.vcf.gz" rule bedtools: input: invcf="/path/to/my.vcf.gz", …
user3224522
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Cannot install bcftools-gtc2vcf-plugin using conda

I have installed bioconda following the instructions at https://bioconda.github.io/user/install.html#set-up-channels. Then I tried conda install bwa conda install bcftools conda install plink2 They all installed fine. However, when I tried conda…
Mousheng Xu
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Fixing segmentation fault error in bcftools

I am trying to merge 3000 bacterial bcf files using bcftools. The vcf files has been generated using GATK and converted to bcf and indexed by bcftools. The bcftools proceeds to analyze 20% of the data but it keeps terminating premature and produces…
Masih
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Else-If Satement with empty variables not working

I'm trying to write a if-else condition in shell/bash script which will be used for many different files so it won't fit a certain structure. I have three different files, and up to three different variables selected from each of these files which…
joeblow
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How to remove snps with missing names

I have 1000 G data set which is in PLINK format, there are some snps with names as ".", is there any way in PLINK i can remove that snps? I tried bcftool view which does not work correctly.
bha
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How to match ID in column in unix?

I am fully aware that similar questions may have been posted, but after searching it seems that the details of our questions are different (or at least I did not manage to find a solution that can be adopted in my case). I currently have two files:…
NeverBe
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Error in Linkdatagen : Use of uninitiated value $chr in concatenation (.) or string

Hi I was trying to use linkdatagen, which is a perl based tool. It requires a vcf file (using mpileup from SAMtools) and a hapmap annotation file (provided). I have followed the instructions but the moment I use the perl script provided, I get this…
SamC
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removing text part between 2 symbols

I have this type of text file (also header, starting with ##, but not shown) #CHROM POS ID REF ALT QUAL FILTER INFO chr1 69511 rs2691305 A G . PASS …
user15480777
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Recommended languages for reading and manipulating BAM and VCF files?

I'm normally a C# / .net developer, but a new project is going to be working with Next Generation Sequencing BAM and VCF files. I will need to read these files, make some changes, and save them. As far as I can tell, there's not much in the way of…
Kyle
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