This repository contains a number of tools created with hts-nim intended
to serve as examples for using hts-nim as well as to be useful tools.
These tools are:
hts-nim utility programs.
version: $version
• bam-filter : filter BAM/CRAM/SAM files with a simple expression language
• count-reads : count BAM/CRAM reads in regions given in a BED file
• vcf-check : check regions of a VCF against a background for missing chunks
each of these is described in more detail below.
Use simple expressions to filter a BAM/CRAM file:
bam-filter
Usage: bam-filter [options] <expression> <BAM-or-CRAM>
-t --threads <threads> number of BAM decompression threads [default: 0]
-f --fasta <fasta> fasta file for use with CRAM files [default: $env_fasta].
valid expressions may access the bam attibutes:
mapq/start/pos/end/flag/insert_size(where pos is the 1-based start)is_alignedis_read1is_read2is_supplementaryis_secondaryis_dupis_qcfailis_reverseis_mate_reverseis_pairis_proper_pairis_mate_unmappedis_unmapped
to use aux tags, indicate them prefixed with 'tag_', e.g.:
tag_NM < 2. Any tag present in the bam can be used in this manner.
example:
bam-filter "tag_NM == 2 && tag_RG == 'SRR741410' && is_proper_pair" tests/HG02002.bam
Count reads reports the number of reads overlapping each interval in a BED file.
count-reads
Usage: count-reads [options] <BED> <BAM-or-CRAM>
Arguments:
<BED> the bed file containing regions in which to count reads.
<BAM-or-CRAM> the alignment file for which to calculate depth.
Options:
-t --threads <threads> number of BAM decompression threads [default: 0]
-f --fasta <fasta> fasta file for use with CRAM files [default: ].
-F --flag <FLAG> exclude reads with any of the bits in FLAG set [default: 1796]
-Q --mapq <mapq> mapping quality threshold [default: 0]
-h --help show help
This is output a line with a count of reads for each line in .
vcf-check is useful as a quality control for large projects which have done variant calling in regions
where each region is called in parallel. With many regions, and large projects, some regions can error and
this might be unknown to the analyst.
This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants. If the background has many variants across a long stretch of genome where the query VCF has no variation, we can expect that region is missed in the query VCF.
Check a VCF against a background to make sure that there are no large missing chunks.
vcf-check
Usage: vcf-check [options] <BACKGROUND_VCF> <VCF>
Arguments:
<BACKGROUND_VCF> population VCF/BCF with expected sites
<VCF> query VCF/BCF to check
Options:
-c --chunk <INT> chunk size for genome [default: 100000]
-m --maf <FLOAT> allele frequency cutoff [default: 0.1]
This will output a tab-delimited file of chrom\tposition\tbackground-count\tquery-count.
The user can find regions that might be problematic by plotting or with some simple awk commands.