Variant calling

SNP calling

snp_rules

medaka consensus

  • Input:
    • BAM file (mapped & sorted reads)
       → provided by samtools sort rule
    • BAI file (mapped & sorted index)
       → provided by samtools index rule
  • Output:
    • HDF file (??)
       → used by medaka snp rule
  • Description:
      ??

medaka snp

  • Input:
    • HDF file (??)
       → provided by medaka consensus rule
    • Fasta file (reference)
  • Output:
    • VCF file (SNP)
       → used by bcftools stats rule
  • Description:
      Call all the SNP between the sample and the reference

SV calling

sv_rules

sniffles

  • Input:
    • BAM file (mapped & sorted reads)
       → provided by samtools sort rule
    • BAI file (mapped & sorted index)
       → provided by samtools index rule
    • FASTA file (reference)
  • Output:
    • VCF file (SV)
       → used by bcftools stats rule
  • Description:
      Call all the SV between the sample and the reference with Sniffles tool

cuteSV

  • Input:
    • BAM file (mapped & sorted reads)
       → provided by samtools sort rule
    • BAI file (mapped & sorted index)
       → provided by samtools index rule
    • FASTA file (reference)
  • Output:
    • VCF file (SV)
       → used by bcftools stats rule
  • Description:
      Call all the SV between the sample and the reference with cuteSV tool

svim

  • Input:
    • BAM file (mapped & sorted reads)
       → provided by samtools sort rule
    • BAI file (mapped & sorted index)
       → provided by samtools index rule
    • FASTA file (reference)
  • Output:
    • VCF file (SV)
       → used by bcftools stats rule
  • Description:
      Call all the SV between the sample and the reference with svim tool

NanoVar

  • Input:
    • BAM file (mapped & sorted reads)
       → provided by samtools sort rule
    • BAI file (mapped & sorted index)
       → provided by samtools index rule
    • FASTA file (reference)
  • Output:
    • VCF file (SV)
       → used by bcftools stats rule
  • Description:
      Call all the SV between the sample and the reference with NanoVar tool

Statistic control

bcftools_rules

bcftools stats

  • Input:
    • VCF file (SNP or SV)
       → provided by medaka snp rule
       → provided by sniffles rule
       → provided by cuteSV rule
       → provided by svim rule
       → provided by NanoVar rule
  • Output:
    • TXT file (VCF stats)
  • Description:
      Compute stats of the variant