Usage¶
EXtract POSitional data and statistics from alignment at
VCF variant sites, and encode them as INFO fields to VCF.
Requires the presence of .(b/cr)ai indexes of the same name
as the relevant alignment. Annotated VCF to stdout. See
README or output VCF header for descriptions of fields
added.
Usage:
expos [OPTION...] <VCF/BCF (- for stdin)> <ALN.(b/cr)am>
-h, --help Print usage
-l, --expected-read-len arg Sequencing read length. Default: 150
-r, --ref arg Alignment Reference Fasta for optionally
adding reference complexity to statistics.
-n, --normal arg Alignment for use as additional background
data for simulation. May be passed multiple
times.
--normal-only Use only reads from the provided normal as
background data, excluding reads from the
sample
-i, --include-records arg Only operate on VCF records with this value
present in FILTER. e.g. -i PASS. May be
passed multiple times.
-e, --exclude-records arg Only operate on VCF records without this
value present in FILTER. May be passed
multiple times.
-I, --include-reads arg SAM flag: only include reads with all of
these bits set. Set 0 to disable. Default: 3
-E, --exclude-reads arg SAM flag: exclude reads with any of these
bits set. Default: 3852
-t, --tsv arg Write a tsv of extended statistics to file
specified.
-u, --uncompressed output uncompressed VCF
--seed arg Set random seed. Default: 24601
--uniform additionally simulate against uniform null
model for query position, and add result to
--tsv output. For assessment of correlation
with simulation against all-reads null.
--assess-microhomology additionally assess STR and homopolymer
content of reference regions, and add result
to --tsv output. For assessment of
correlation with drop in LZ.
--debug Enable debug logging
Basic usage: