Common Alignment Stats

Calculated for one or more bam file.

Current Stats:

name

Sample name. If two bam files have the same name,
name will be appended by incrementing integer

single_mapped_reads

Number of reads from the fastq file that align
to only one location in the reference genome.
Found by counting number of reads with NH:i:1

single_mapped_reads_percent

single_mapped_reads / total_alignable_reads

multi_mapped_reads

Number of reads from the fastq file that align
to multiple locations in the reference genome

multi_mapped_reads_percent

multi_mapped_reads / total_alignable_reads

total_alignable_reads

single_mapped_reads + multi_mapped_reads

primary_alignments

Count of total uniquely named alignments in bam file.
Each alignable read is counted once for this measure.
This is really just Total alignable reads, but
described in the context of the alignment.

secondary_alignments

Count of Additional alignments in bam file from
multi-mapped reads.
Found by looking for 0×100 flag in alignments

total_alignments

primary_alignments + secondary_alignments.

total_reads_in_bam

Total number of lines in bam file. For a bam
file that does not include unaligned data,
this should be the same as total_alignments

unique_positions

Total number of unique alignment positions found
for alignments in bam file.
Assumes bam file is position sorted.

Timing

Currently bam_stats can analyze 80,000 reads per second. Compare this to a standard samtools view of all reads, which can be done at around 280,000 reads per second.

reads	bam_stats	wc	bam_stats/sec	wc/sec
41786101	516.94	147	80,834	284,259
108153984	1279.62	402	84,520	269,040
31279258	371.85	115	84,118	271,994
235991688	2785	842	84,737	280,275