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vcf.md

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VCF output from Straglr

  • VCFv4.5 specification followed
  • Sample name (--sample) must be provided (otherwise . will be used as sample name)
  • <CNV:TR> will be used for all ATL alleles, no <CNV:TR> will be reported for REF alleles
  • RUS reported for STRs (motif length 2-6bp) and RUL for VNTRs, following v4.5 recommendation
  • RB (allele length) will be reported if --genotype_in_size was specified, otherwise RUC (copy number) will be reported
  • SVLEN equals length (bp) of the reference allele, not the difference between start and end coordinate
  • RUS_REF and RUL_REF added to INFO fields to indicate motif sequence (for STRs) and motif lengths (for VNTRs), as variants may exhibit different motifs
  • CIRUB and CIRB were based on minimum and maximum values detected in all support reads for each allele (reported in TSV file)
  • currently RN is always 1 as complex TRs are not supported

FILTER

Loci requested for genotyping (specified in --loci) may fail and one of the filters (besides PASS) was assigned

Name Description
PASS All filters passed
UNMATCHED_MOTIF motif detected is not the same as the specified motif
PARTIAL_SPAN repeat detected not spanning majority (90%) locus
INVALID_MOTIF motif detected outside motif size range
CLUSTERING_FAILED clustering failed to formulate genotype

INFO

Field Description
LOCUS Locus ID: fourth column (after chrom, statrt, end, motif) in BED file from parameter --loci e.g. gene name
RUS_REF Motif sequence detected by TRF on reference sequence if STR reported
RUL_REF Motif length (bp) detected by TRF on reference sequence if VNTR reported
SVLEN Allele length of reference sequence as determined by TRF
RN Number of motifs in each allele, currently always 1 as complex motifs are not supported
RUS Motif sequences of each allele, currently alway one sequence for each allele
RUL Length of motif sequences reported in RUS
RUC Copy number of each motif in RUS, reported when --genotype_in_size is not used
RB Number of bases for each motif in RUS, reported when --genotype_in_size is used
CIRUC Differences between lower and upper bounds in all support reads from RUC in each RUS
CIRB Differences between lower and upper bounds in all support reads from RB in each RUS

FORMAT

Field Description
GT Genotype: reference (0) assigned when reference size (determined by TRF, not SVLEN) is within size range (10% added to boundaries) of allele closest in size to reference
DP Read depth: number of reads spanning locus (= coverage column in TSV output)
AD Allelic depths: number of support reads for each allele