alignment

The following tools are grouped under alignment as they take alignment files (.bam) as input.

bam

Given a bam file as input, compute the following general alignment statistics and output them as json. The output will contain the following fields:

field	description
Input reads	total number of reads in the BAM file
Mapped	total number of reads mapped to the reference genome
Unmapped	total number of reads that are not mapped

Options

option	description	required	default value
–bam	Path to the input bam file (MUST be co-ordinate sorted and indexed)	✓
–out-json	Output file to write json formatted data	✓
–min-q	Minimum alignment quality	✗	0

Usage

ngs-statter bam --bam path/to/alignment.bam --out-json path/to/output.json --min-q 0

STAR

Compute alignment statistics for an alignment file generated using STAR aligner and output as json. The output will contain the following fields:

field	description
Reads for mapping	total number of reads in the BAM file
Mapped: Total	total number of reads mapped to the reference genome
Mapped: Uniquely mapped reads	total number of reads mapped to a unique location in the reference genome
Mapped: Multimapped reads	total number of reads mapped to multiple locations in the reference genome
Mapped: PCR duplicate reads	total number of mapped reads marked as PCR duplicates in the BAM file, if the BAM file is marked for duplicates, see samtools markdup
Mapped: Unique reads	total number of reads mapped to a unique location in the reference genome and not marked as PCR duplicates in the BAM file, if the BAM file is marked for duplicates, see samtools markdup
Unmapped: Total	total number of reads that are not mapped to the reference genome
Unmapped: mapped to too many loci	total number of reads that marked as unmapped as they are mapped to too many locations in the reference genome
Unmapped: no seed/windows	total number of reads that are marked as unmapped as they do not have a seed region that can be mapped to the reference genome
Unmapped: too many mismatches	total number of reads that are marked as unmapped as they have too many mismatches compared to the reference genome
Unmapped: too short	total number of reads that are marked as unmapped as the seed regions are too short to be mapped to the reference genome
Unmapped: paired-end mate	for paired end reads, total number of reads that are marked as unmapped as their paired end mate is mapped to the reference genome

Options

option	description	required	default value
–bam	Path to the input bam file (MUST be co-ordinate sorted and indexed)	✓
–out-json	Output file to write json formatted data	✓
–min-q	Minimum alignment quality	✗	0

Usage

ngs-statter STAR --bam path/to/star_alignment.bam --out-json path/to/output.json --min-q 0