Little toolset operating over VCF files. Uses cyvcf2 and cython under the hood for speed.
vtools is now on pip! Since the 'vtools' name is already taken by another package, installing this vtools requires installing the following:
pip install v-toolsAfter installation, tools will still be called vtools-<tool>. Programmatic
access also simply works with
import vtoolsconda install -c bioconda vtoolsFilter VCF files based on a few criteria. Will output both a filtered VCF file, and a VCF file containing all the filtered-out variants.
| name | meaning | optional |
|---|---|---|
| NON_CANONICAL | Non-canonical chromosome | Yes |
| INDEX_UNCALLED | Index uncalled or homozygous reference | Yes |
| TOO_HIGH_GONL_AF | Too high GonL allele frequency | Yes |
| TOO_HIGH_GNOMAD_AF | Too high GnomAD allele frequency | Yes |
| LOW_GQ | Too low GQ on index sample | Yes |
| DELETED_ALLELE | The only ALT allele is a deleted allele | No |
Configuration of filters goes by a little JSON file. See here for an example.
Usage: vtools-filter [OPTIONS]
Options:
-i, --input PATH Path to input VCF file [required]
-o, --output PATH Path to output (filtered) VCF file
[required]
-t, --trash PATH Path to trash VCF file [required]
-p, --params-file PATH Path to filter params json [required]
--index-sample TEXT Name of index sample [required]
--immediate-return / --no-immediate-return
Immediately write filters to file upon
hitting one filter criterium. Default = True
--help Show this message and exit.
Collects some general statistics about a VCF file, and writes a json to stdout.
Usage: vtools-stats [OPTIONS]
Options:
-i, --input FILE Input VCF file [required]
--help Show this message and exit.Collect coverage metrics over a gVCF file for every exon or every transcript in a refFlat file. This assumes the input VCF file is at least similar to GATK's gVCF files. gVCF files are only expected to have one sample; if your input file contains multiple samples, we simply take the first only.
Output is a simple TSV file with the following columns
| column | meaning |
|---|---|
| exon | exon number |
| gene | gene name / symbol / id |
| mean_dp | mean DP value over the exon |
| mean_gq | mean GQ value over the exon* |
| median_dp | median DP value over the exon |
| median_gq | median GQ value over the exon |
| perc_at_least_{10, 20, 30, 50, 100}_dp | Percentage of exon with DP value over value |
| perc_at_least_{10, 29, 30, 50, 90}_gq | Percentage of exon with GQ value over exon |
| transcript | transcript name / symbol / id |
*: mean GQ value is computed by first calculating the P-value of all GQ values, then calculating the mean over these P-values, and lastly converting this number back to a phred score.
Usage: vtools-gcoverage [OPTIONS]
Options:
-I, --input-gvcf PATH Path to input VCF file [required]
-R, --refflat-file PATH Path to refFlat file [required]
--per-exon / --per-transcript Collect metrics per exon or per transcript
--help Show this message and exit.Evaluate a VCF file to a baseline VCF file containing true positives. We only consider variants that are present in both VCF files. This makes it useful when the two VCF files have been produced by wildly different technologies. E.g, when comparing a WES VCF file vs a SNP array, this tool can be quite useful.
Output is a simple JSON file listing counts of concordant and discordant alleles and some other metrics. It is also possible to output the discordant VCF records.
Multisample VCF files are allowed; the samples to be evaluated have to be set through a CLI argument.
Variants from the --call-vcf are filtered to have a Genotype Quality (GQ) of
at least 30 by default. This can be overruled by specifying --min-qual 0.
The optional flag --min-depth can be used to set the minimum read coverage.
Usage: vtools-evaluate [OPTIONS]
Options:
-c, --call-vcf PATH Path to VCF with calls to be evaluated
[required]
-p, --positive-vcf PATH Path to VCF with known calls [required]
-cs, --call-samples TEXT Sample(s) in call-vcf to consider. May be
called multiple times [required]
-ps, --positive-samples TEXT Sample(s) in positive-vcf to consider. May be
called multiple times [required]
-s, --stats PATH Path to output stats json file
-dc, --discordant PATH Path to output gzipped discordant vcf file
-mq, --min-qual FLOAT Minimum quality of variants to consider
-md, --min-depth INTEGER Minimum depth of variants to consider
--help Show this message and exit.MIT