gmapR (version 1.14.0)

bam_tally-methods: Per-position Alignment Summaries

Description

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.

Usage

"bam_tally"(x, param, ...)
"bam_tally"(x, param, ...)
variantSummary(x, read_pos_breaks = NULL, keep_ref_rows = FALSE, read_length = NA_integer_, high_nm_score = NA_integer_)

Arguments

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.

Value

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.

See Also

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