Plugin vrfs
This plugin can be used to assess site noisiness from a large number of unaffected parental samples. It generates the variant read frequency score (VRFS) which quantifies recurrence of the alternate allele across unrelated samples, enabling identification of loci that most likely reflect sequencing artefacts or, if truly recurrent, are unlikely to be clinically relevant.
For more information and math notes see PAPER.
The list of plugin-specific options can be obtained by running
bcftools +vrfs, which will print the following usage page:
Usage: bcftools +vrfs [OPTIONS]
Required options:
-a, --alns FILE List of BAM/CRAM files
-f, --fasta-ref FILE Reference file in fasta format
-s, --sites FILE A tab-delimited file name of sites to assess (chr,pos,ref,alt)
Model options:
-d, --min-depth INT Minimum depth of calls to include in the profile [10]
-n, --nbins INT Number of VAF bins [20]
-r, --recalc TYPE Recalculate scores based on provided variances [hc]
data .. as observed in the data
file .. read profile from a file, one value per line (-r file:/path/to/file.txt)
hc .. hard-coded profile
Other options:
-b, --batch I/N Run I-th batch out of N, 1-based
-i, --use-index Use index to jump the alignments, rather than stream (faster with few sites)
-m, --merge-batches FILE Merge files produced with -b, --batch, FILE is a list of batch files
-M, --merge-files FILE ... Same as -m, FILE is one or more batch files
-o, --output FILE Output file name [stdout]
-O, --output-type t|z[0-9] t/z: un/compressed text file, 0-9: compression level [t]
-v, --verbosity INT Verbosity level, eg can print the elapsed and estimated total running time
Example:
# Typical run
bcftools +vrfs -f ref.fa -a bams.txt -s sites.txt -o scores.txt
# Run in batches. Let's say one batch can have at most 3 bams and there are 5 bams in total
# 1) find out the number of required batches with `--batch k=3` (the program outputs: 2)
# 2) run all batches individually with `--batch 1/2` and `--batch 2/2`
# 3) create a list of outputs and merge with `--merge-batches list.txt`
bcftools +vrfs -a bams.txt --batch k=3 # prints 2
bcftools +vrfs -f ref.fa -a bams.txt -s sites.txt -o scores1.txt --batch 1/2
bcftools +vrfs -f ref.fa -a bams.txt -s sites.txt -o scores2.txt --batch 2/2
bcftools +vrfs --merge-batches list.txt
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