Small Variant output files¶
The workflow will create the following in the directory you launch the pipeline from.
Intermediate output is written to the working directory, on HPC /re_scratch/$USER (default -work-dir)
For each query gene and build, the main output is an annotated list of variants, and a multi-sample VCF file and index.
GENOMEBUILD_HGNCSYMBOL_ENSEMBLID_annotated_variants.tsv
GENOMEBUILD_HGNCSYMBOL_ENSEMBLID_left_norm_tagged.vcf.gz
GENOMEBUILD_HGNCSYMBOL_ENSEMBLID_left_norm_tagged.vcf.gz.tbi
--publish_all true, the output of every process is written to a folder with process name, within results/ (default --outdir).
Additional INFO tags¶
Additional bcftools INFO tags are computed with the plugin fill-tags. These per variant tags are derived from the merged single-sample VCF and combined with the VEP annotation output in the final annotated variant file.
| ID | Description | Meaning |
|---|---|---|
| AN | Total number of alleles in called genotypes | |
| AC | Allele count in genotypes | |
| NS | Number of samples with data | The number of samples which have been included for a particular variant, and is equal to the number of samples with any variant at the given chromosomal position |
| AC_Hom | Allele counts in homozygous genotypes | The number of alleles for the given variant counted from the genotypes listed in the multi-sample VCF |
| AC_Het | Allele counts in heterozygous genotypes | |
| AC_Hemi | Allele counts in hemizygous genotypes | |
| MAF | Frequency of the second most common allele |
Annotated variant file columns¶
- *_variant columns are
bcftoolsoutput - *_annotation columns are
VEPannotation output - *_sample columns derived from filtering on bi-allelic genotype
| Name | Description |
|---|---|
| CHROM_variant | chromosome |
| POS_variant | position |
| ID_variant | identifier |
| REF_variant | reference base(s) |
| ALT_variant | alternate base(s) |
| (...) | bcftools +fill-tags columns described above |
| DUP_variant | |
| (...) | VEP annotation output |
| Het_samples | samples from output VCF selected with bcftools -i 'GT="het"' |
| Hom_samples | samples from output VCF selected with bcftools -i 'GT="AA"' |
| Hemi_samples | samples from output VCF selected with bcftools -i 'GT="A"' |