gtc2vcf

A set of tools to convert Illumina and Affymetrix DNA microarray intensity data files into VCF files <b>without</b> using Microsoft Windows. You can use the final output to run the pipeline to detect mosaic chromosomal alterations. If you use this tool in your publication, please cite this website. For any feedback or questions, contact the author

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• Usage
• Installation
• Software Installation
• Identifying chip type for IDAT and CEL files
• Convert Illumina IDAT files to GTC files
• Convert Illumina GTC files to VCF
• Convert Affymetrix CEL files to CHP files
• Convert Affymetrix CHP files to VCF
• Using an alternative genome reference
• Detect contamination
• Plot variants
• Illumina GenCall
  • Illumina AutoConvert
  • Illumina AutoConvert 2.0
  • Illumina Array Analysis Platform Genotyping Command Line Interface
  • Illumina Microarray Analytics Array Analysis Command Line Interface
• Acknowledgements

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Usage

Illumina data tool:

Usage: bcftools +gtc2vcf [options] [<A.gtc> ...]

Plugin options:
    -l, --list-tags                   list available FORMAT tags with description for VCF output
    -t, --tags LIST                   list of output FORMAT tags [GT,GQ,IGC,BAF,LRR,NORMX,NORMY,R,THETA,X,Y]
    -b, --bpm <file>                  BPM manifest file
    -c, --csv <file>                  CSV manifest file (can be gzip compressed)
    -e, --egt <file>                  EGT cluster file
    -f, --fasta-ref <file>            reference sequence in fasta format
        --set-cache-size <int>        select fasta cache size in bytes
        --gc-window-size <int>        window size in bp used to compute the GC content (-1 for no estimate) [200]
    -g, --gtcs <dir|file>             GTC genotype files from directory or list from file
    -i, --idat                        input IDAT files rather than GTC files
        --capacity <int>              number of variants to read from intensity files per I/O operation [32768]
        --adjust-clusters             adjust cluster centers in (Theta, R) space (requires --bpm and --egt)
        --use-gtc-sample-names        use sample name in GTC files rather than GTC file name
        --do-not-check-bpm            do not check whether BPM and GTC files match manifest file name
        --do-not-check-eof            do not check whether the BPM and EGT readers reach the end of the file
        --genome-studio <file>        input a GenomeStudio final report file (in matrix format)
        --no-version                  do not append version and command line to the header
    -o, --output <file>               write output to a file [standard output]
    -O, --output-type u|b|v|z|t[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF
                                      t: GenomeStudio tab-delimited text output, 0-9: compression level [v]
        --threads <int>               number of extra output compression threads [0]
    -x, --extra <file>                write GTC metadata to a file
    -v, --verbose                     print verbose information
    -W, --write-index[=FMT]           Automatically index the output files [off]

Manifest options:
        --beadset-order               output BeadSetID normalization order (requires --bpm and --csv)
        --fasta-flank                 output flank sequence in FASTA format (requires --csv)
    -s, --sam-flank <file>            input flank sequence alignment in SAM/BAM format (requires --csv)
        --genome-build <assembly>     genome build ID used to update the manifest file [GRCh38]

Examples:
    bcftools +gtc2vcf -i 5434246082_R03C01_Grn.idat
    bcftools +gtc2vcf 5434246082_R03C01.gtc
    bcftools +gtc2vcf -b HumanOmni2.5-4v1_H.bpm -c HumanOmni2.5-4v1_H.csv
    bcftools +gtc2vcf -e HumanOmni2.5-4v1_H.egt
    bcftools +gtc2vcf -c GSA-24v3-0_A1.csv -e GSA-24v3-0_A1_ClusterFile.egt -f human_g1k_v37.fasta -o GSA-24v3-0_A1.vcf
    bcftools +gtc2vcf -c HumanOmni2.5-4v1_H.csv -f human_g1k_v37.fasta 5434246082_R03C01.gtc -o 5434246082_R03C01.vcf
    bcftools +gtc2vcf -f human_g1k_v37.fasta --genome-studio GenotypeReport.txt -o GenotypeReport.vcf

Examples of manifest file options:
    bcftools +gtc2vcf -b GSA-24v3-0_A1.bpm -c GSA-24v3-0_A1.csv --beadset-order
    bcftools +gtc2vcf -c GSA-24v3-0_A1.csv --fasta-flank -o GSA-24v3-0_A1.fasta
    bwa mem -M GCA_000001405.15_GRCh38_no_alt_analysis_set.fna GSA-24v3-0_A1.fasta -o GSA-24v3-0_A1.sam
    bcftools +gtc2vcf -c GSA-24v3-0_A1.csv --sam-flank GSA-24v3-0_A1.sam -o GSA-24v3-0_A1.GRCh38.csv

Affymetrix data tool:

Usage: bcftools +affy2vcf [options] --csv <file> --fasta-ref <file> [<A.chp> ...]

Plugin options:
    -l, --list-tags                 list available FORMAT tags with description for VCF output
    -t, --tags LIST                 list of output FORMAT tags [GT,CONF,BAF,LRR,NORMX,NORMY,DELTA,SIZE]
    -c, --csv <file>                CSV manifest file (can be gzip compressed)
    -f, --fasta-ref <file>          reference sequence in fasta format
        --set-cache-size <int>      select fasta cache size in bytes
        --gc-window-size <int>      window size in bp used to compute the GC content (-1 for no estimate) [200]
        --probeset-ids              tab delimited file with column 'probeset_id' specifying probesets to convert
        --calls <file>              apt-probeset-genotype calls output (can be gzip compressed)
        --confidences <file>        apt-probeset-genotype confidences output (can be gzip compressed)
        --summary <file>            apt-probeset-genotype summary output (can be gzip compressed)
        --snp <file>                apt-probeset-genotype SNP posteriors output (can be gzip compressed)
        --chps <dir|file>           input CHP files rather than tab delimited files
        --cel <file>                input CEL files rather CHP files
        --adjust-clusters           adjust cluster centers in (Contrast, Size) space (requires --snp)
        --no-version                do not append version and command line to the header
    -o, --output <file>             write output to a file [standard output]
    -O, --output-type u|b|v|z[0-9]  u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]
        --threads <int>             number of extra output compression threads [0]
    -x, --extra <file>              write CHP metadata to a file (requires CHP files)
    -v, --verbose                   print verbose information
    -W, --write-index[=FMT]         Automatically index the output files [off]

Manifest options:
        --fasta-flank               output flank sequence in FASTA format (requires --csv)
    -s, --sam-flank <file>          input flank sequence alignment in SAM/BAM format (requires --csv)

Examples:
    bcftools +affy2vcf \
        --csv GenomeWideSNP_6.na35.annot.csv \
        --fasta-ref human_g1k_v37.fasta \
        --chps cc-chp/ \
        --snp AxiomGT1.snp-posteriors.txt \
        --output AxiomGT1.vcf \
        --extra report.tsv
    bcftools +affy2vcf \
        --csv GenomeWideSNP_6.na35.annot.csv \
        --fasta-ref human_g1k_v37.fasta \
        --calls AxiomGT1.calls.txt \
        --confidences AxiomGT1.confidences.txt \
        --summary AxiomGT1.summary.txt \
        --snp AxiomGT1.snp-posteriors.txt \
        --output AxiomGT1.vcf

Examples of manifest file options:
    bcftools +affy2vcf -c GenomeWideSNP_6.na35.annot.csv --fasta-flank -o  GenomeWideSNP_6.fasta
    bwa mem -M GCA_000001405.15_GRCh38_no_alt_analysis_set.fna GenomeWideSNP_6.fasta -o GenomeWideSNP_6.sam
    bcftools +affy2vcf -c GenomeWideSNP_6.na35.annot.csv -s GenomeWideSNP_6.sam -o GenomeWideSNP_6.na35.annot.GRCh38.csv

Installation

Install basic tools (Debian/Ubuntu specific if you have admin privileges)

sudo apt install wget unzip git g++ zlib1g-dev bwa unzip samtools msitools cabextract mono-devel libgdiplus icu-devtools bcftools

Optionally, you can install these libraries to activate further HTSlib features

sudo apt install libbz2-dev libssl-dev liblzma-dev libgsl0-dev

Preparation steps

mkdir -p $HOME/bin $HOME/GRCh3{7,8} && cd /tmp

We recommend compiling the source code but, wherever this is not possible, Linux x86_64 pre-compiled binaries are available for download here. However, notice that you will require BCFtools version 1.20 or newer. You can also download a previous version of the plugin through bioconda

Download latest version of HTSlib and BCFtools (if not downloaded already)

wget http://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
tar xjvf bcftools-1.20.tar.bz2

Download and compile plugins code (make sure you are using gcc version 5 or newer)

cd bcftools-1.20/
/bin/rm -f plugins/{idat2gtc.c,gtc2vcf.{c,h},affy2vcf.c}
wget -P plugins http://raw.githubusercontent.com/freeseek/gtc2vcf/master/{idat2gtc.c,gtc2vcf.{c,h},affy2vcf.c,BAFregress.c}
make
/bin/cp bcftools plugins/{idat2gtc,gtc2vcf,affy2vcf,BAFregress}.so $HOME/bin/

Make sure the directory with the pl