GSTRUCT suite

Description Usage Arguments Value Author(s) See Also

Given a set of alignments, for each position in the genome output counts for the reference allele and all alternate alleles. Often used as a precursor to detecting variants. Indels will be supported soon.

## S4 method for signature 'BamFile'
bam_tally(x, param, ...)
## S4 method for signature 'character'
bam_tally(x, param, ...)
variantSummary(x, read_pos_breaks = NULL,
               keep_ref_rows = FALSE, read_length = NA_integer_,
               high_nm_score = NA_integer_)

`x`	a `BamFile` object or string path to a BAM file to read
`param`	The `BamTallyParam` object with parameters for the tally operation.
`read_pos_breaks`	The breaks, like those passed to `cut` for aggregating the per-read position counts. If `NULL`, no per-cycle counts are returned.
`keep_ref_rows`	Whether to keep the rows describing only the reference calls, i.e., where ref and alt are the same. These are useful when one needs the reference counts even when there are no alts at that position.
`read_length`	The expected read length. If the read length is NA, the MDFNE (median distance from nearest end) statistic will NOT be calculated.
`high_nm_score`	The value at which an NM value is considered high.
`...`	Arguments that override settings in `param`.

The bam_tally function returns an opaque pointer to a C-level data structure with the class “TallyIIT”. Currently, the only operation applicable to this object is variantSummary.

The variantSummary function returns a VRanges, with a range for each position that passed the filters. The depth columns correspond to the counts after quality filtering (except for indels, for which there is no quality filtering). The following elementMetadata columns are also present:

`n.read.pos`	The number of unique read positions for the alt allele.
`n.read.pos.ref`	The number of unique read positions for the ref allele.
`raw.count.total`	The total number of reads at that position, including reference and all alternates.
`count.plus`	The number of positive strand reads for the alternate allele, `NA` for the reference allele row.
`count.plus.ref`	The number of positive strand reads for the reference allele.
`count.minus`	The number of negative strand reads for the alternate allele, `NA` for the reference allele row.
`count.minus.ref`	The number of negative strand reads for the reference allele.
`count.del.plus`	The plus strand deletion count over the position.
`count.del.minus`	The minus strand deletion count over the position.
`read.pos.mean`	Mean read position for the alt allele.
`read.pos.mean.ref`	Mean read position for the ref allele.
`read.pos.var`	Variance in the read positions for the alt allele.
`read.pos.var.ref`	Variance in the read positions for the ref allele.
`mdfne`	Median distance from nearest end for the alt allele.
`mdfne.ref`	Median distance from nearest end for the ref allele.
`count.high.nm`	The number of alt reads with an NM value at or above the `high_nm_score` cutoff.
`count.high.nm.ref`	The number of ref reads with an NM value at or above the `high_nm_score` cutoff.

If codon counting was enabled, there will be a column giving the codon strand: codon.strand.

If the xs parameter was TRUE, there will be four additional columns giving the counts by aligner-determined strand: count.xs.plus, count.xs.plus.ref, count.xs.minus, and count.xs.minus.ref.

An additional column is present for each bin formed by the read_pos_breaks parameter, with the read count for that bin.

Michael Lawrence

tallyVariants in the VariantTools package provides a high-level wrapper for this functionality.

gmapR documentation built on Nov. 8, 2020, 5:29 p.m.