Tools

  • Gene ID conversion between Kronos and CS
  • Find wheat potential homeologs
  • Extract cDNA sequences
  • Short read de novo assembly with Velevet
  • CRISPR editing check with BWA and SAMTOOLS v2
  • CRISPR NGS editing check with HISAT2
  • Make bam files with strobeAlign
  • Shade sequence alignments with nimBoxshade
  • Shade sequence alignments with Boxshade
  • Design KASP primers with Primer3 v2.5.0
  • Convert a vcf file to SNP table
  • Call variants with exactSNP
  • Index bams with SAMTOOLS
  • Format FASTA to fixed length
  • Make bams and indel calls with Subread
  • Filter fastq files with FASTP
  • Filter multiple fastq files with FASTP
  • Make bam files with BWA and SAMTOOLS
  • CRISPR Editing Analysis v2
  • Demultiplex a Fastq File
  • CRISPR Editing Analysis
  • Call SNPs from multiple sequence alignment
  • Reverse complement of DNA sequences

    • Convert a vcf file to SNP table

    This is a simple tool to convert a vcf file to SNP table.

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    Help

    Output includes:

    CHROM: chromosome
    POS: position
    REF: reference allele
    ALT: alternative alleles (mutations compared to the reference)
    QUAL: variant quality (the more reads and more counts of ALT alleles, the higher quality)
    AC: “Allele count in genotypes, for each ALT allele, in the same order as listed”
    AN: “Total number of alleles in called genotypes”; AN/2 = number of lines with data
    DP: total reads; “Approximate read depth; some reads may have been filtered”
    MQ: Mapping Quality

    Then genotying data of each line: N is missing and H is heterozygous.