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Questions tagged [vcftools]

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

This toolset can be used to perform the following operations on VCF files:

  • Filter out specific variants
  • Compare files
  • Summarize variants
  • Convert to different file types
  • Validate and merge files
  • Create intersections and subsets of variants

Links:

  1. Home page

  2. Documentation

  3. Github

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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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Apache Kafka and Nifi for processing a VCF file

I am trying to parse a VCF file using the Apache Kafka and Nifi tools, basically the VCF is available in a file system and I have to acquire and parse to extract the different attributes from it. Is it advisable to use Apache Kafka and/or Nifi for…
Vishnu
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How to fix this error when installing bcftools on MAC? Problem with C: [ploidy.o] Error 1

I am trying to install bcftools on the Mac for the handling of VCF files, but I have some problems when performing a correct installation of this, specifically when doing 'make'. The instructions for the installation of bfctools appear in the…
Vásquez Carlos
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Empty ggplot from .txt

I'm trying to do a plot from a file generated with the vcftools program at linux. The file looks like: CHROM BIN_START SNP_COUNT VARIANTS/KB chr0 0 46 4.6 chr0 10000 34 3.4 chr0 20000 0 0 chr0 30000 21 2.1 chr0 …
J0ki
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Can't locate Bio/SeqIO.pm in @INC

Hi I am trying to install VelvetOptimizer using docker. and it say Can't locate Bio/SeqIO.pm in @INC. It requires the following to be installed: Velvet >= 0.7.51 ,Perl >= 5.8, BioPerl >= 1.4 and i have installed them Please find the…
nad87563
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Cannot convert ‘bool’ to ‘gzFile {aka gzFile_s*}’

I am new to Linux environments, and trying to install a bioinformatics package (vcftools - https://vcftools.github.io/examples.html). For some reason I can compile without a problem in a Cygwin environment, other colleagues have installed the…
user1885116
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how to squeeze -1 in file

I have a file like following -1 1 -1 2 -1 2 -1 2 0 I want to squeeze the element "-1" by tr -s '-1' file But it does not work. ADDED I use vcftools to change vcf.gz to matrix with element "0", "1", or "2"(say,chr1.012) (missing value will be…
81235
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Redirecting vcftools file in linux - tips

Here is the code that gets the VCF file from a specific region using tabix and then filters it for specific (european) population using 'keep' option from vcftools. ####select specific population if [ "$POP_FILE" != "" ]; then vcftools --vcf…
MrMsarguru
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Continually adding to a string given different if else statements [R]

I have a convoluted problem, and I hope I can explain it easily... I have the following data: CHROM POS REF SNP INDEL 5 290 A --|T|--|-- 0 5 890 A A|T|--|G 0 7 672 A …
user2726449
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Slow python code to parse VCF file and insert in database

I have the following code which is written to parse VCF (Variant call format) file: Python code: import vcf import psycopg2 datalist = [] def create_snp_tables() : drop_table_query = 'DROP TABLE IF EXISTS sampletable;' …
dang
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Genetic differentiation in R, function genetic_diff()

I'm trying to run the function genetic_diff(): myDiff <- genetic_diff(vcf, pops = pop, method = 'nei') But I get the following information " if(class(x) != "vcfR"){ stop(paste("Expecting an object of class vcfR, instead received", class(vcf)))" What…
A. Martins
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