vartovcf

Convert variants from VarDict/VarDictJava into VCF v4.2 format.

❯ VarDictJava/build/install/VarDict/bin/VarDict \
    -b input.bam \
    -G /references/hg38.fa \
    -N dna00001 \
    -c1 -S2 -E3 -g4 -f0.05 \
    --fisher \
    calling-intervals.bed \
  | vartovcf -r /references/hg38.fa -s dna00001 \
  | bcftools sort -Oz > variants.vcf.gz

Features

• Unlike the Perl script bundled with VarDict, this tool streams record-by-record
• This tool is kept lean on purpose and is solely responsible for fast format conversion
• The output is compliant with the VCF v4.2 and v4.3 specifications
• Output VCF records are unsorted and a call to bcftools sort is recommended
• At this time, only tumor-only mode (var2vcf_valid.pl) is supported

Benchmarks

❯ vartovcf -r /references/hs38DH.fa -s dna00001 < test.var > /dev/null
[2021-01-31T03:45:12Z INFO  vartovcf] Input stream: STDIN
[2021-01-31T03:45:12Z INFO  vartovcf] Output stream: STDOUT
[2021-01-31T03:45:12Z INFO  vartovcflib::progress_logger] Logging records started at: 2021-01-30 22:45:12.
[2021-01-31T03:45:17Z INFO  vartovcflib::progress_logger] Processed 100000 variant records. Elapsed time: 00:00:05. Time of last 100000 variant records: 00:00:05
[2021-01-31T03:45:21Z INFO  vartovcflib::progress_logger] Processed 156471 variant records. Elapsed time: 00:00:08. Time of last 56471 variant records: 00:00:03

❯ hyperfine --warmup 5 'vartovcf -r /references/hs38DH.fa -s dna00001 < test.var > /dev/null'
Benchmark #1: vartovcf -r /references/hs38DH.fa -s dna00001 < test.var > /dev/null
  Time (mean ± σ):      1.565 s ±  0.043 s    [User: 1.543 s, System: 0.019 s]
  Range (min … max):    1.528 s …  1.679 s    10 runs

❯ hyperfine --warmup 5 'var2vcf_valid.pl -N dna00001 -f 0.0 -E < test.var > /dev/null'
Benchmark #1: var2vcf_valid.pl -N dna00001 -f 0.0 -E < test.var > /dev/null
  Time (mean ± σ):      1.815 s ±  0.021 s    [User: 1.680 s, System: 0.128 s]
  Range (min … max):    1.789 s …  1.848 s    10 runs