Bioinformatic tool for sam and vsf file formats manipulation

Bioinformatic tool for filtering and manipulating sam/bam alignment, vcf/bcf variant calling and fastq files.

Python modules requirements

You need to have Python version >=3.0 and the following modules installed:
numpy
pysam

Usage instructions

Run the provided bioinformatic_formats_tool.py script with Python3 on one of the following bioinformatic formatted files: sam or bam (sequence alignment file or its binary ver, produced with short reads aligners such as Bowtie2 or BWA), vcf or bcf (variant calling file or its binary ver, produced with variant/SNP callers such as SAMtools or BCFtools), or illumina raw fastq files.
Using this script, you can filter your sam/bam files according to different criteria such as read base Phred quality, mapping quality, %-alignment identity, read length or by specific reference. You can obtain mapping statistics, sort and index your bam file or extract only reads flagged as "mapped" (similar functionality to SAMtools program). You can also filter vcf/bcf variants files. Finally, another useful things you can do is to convert your bam file back to fastq file, convert 2 paired-end fastq files (forward/reverse) to a single interleaved fastq file, and convert fastq to fasta format (without Phred base scores).

Full command-line options (--help)

usage: bioinformatic_formats_tool.py [-h] -o <path-to-output> [-b] [-r REF_MATCH] [-mq <1-43>] [-rq <1-40>] [-p <0-100>] [-l READ_LEN] [-s] [-m] [-so] [-ix] [-fs] [-bf]
                                     [--fastq-filter <min-length min-quality> <min-length min-quality>] [-fc] [-ff] [-v <ref-name read-depth map-qual> [<ref-name read-depth map-qual> ...]]
                                     <input file> [<input file> ...]

Bioinformatic software tool for filtering and manipulating sam/bam alignment, bcf/vcf variant calling and fastq files; version 0.2. Author: Vadim (Dani) Dubinsky ([email protected])

positional arguments:
  <input file>          input file (sam/bam/vcf/bcf/fastq) or files (paired fastq)

optional arguments:
  -h, --help            show this help message and exit
  -o <path-to-output>, --output <path-to-output>
                        path to output directory
  -b, --bam-filter      apply bam filter, select from the next 5 parameters (default: retain all reads)
  -r REF_MATCH, --ref-match REF_MATCH
                        bam filter, reads mapped to specific reference, wildcards (*) and regexp can be used
  -mq <1-43>, --map-qual <1-43>
                        bam filter, reads above a mapping quality (MAPQ) threshold
  -rq <1-40>, --read-qual <1-40>
                        bam filter, reads above a mean Phred score threshold
  -p <0-100>, --pident <0-100>
                        bam filter, reads above percent identity between the reads and reference
  -l READ_LEN, --read-len READ_LEN
                        bam filter, reads above a length threshold
  -s, --mapread-stats   Calculate reads mapping per each reference contig/gene
  -m, --mapped-reads    extract only mapped reads (for sam/bam files)
  -so, --sort           samtools sort command (for sam/bam files)
  -ix, --index          samtools index command (for sam/bam files)
  -fs, --flagstat       samtools flagstat command (for sam/bam files, output reads mapping summary stats)
  -bf, --bamtofastq     convert a bam to fastq file (paired reads interleaved in a single file)
  --fastq-filter <min-length min-quality> <min-length min-quality>
                        filter a single fastq or two paired fastq file/s based on read length and mean Phred score quality
  -fc, --fastq-concat   convert 2 paired-end fastq files to a single interleaved file
  -ff, --fastq-fasta    convert fastq file to fasta format
  -v <ref-name read-depth map-qual> [<ref-name read-depth map-qual> ...], --vcf-filter <ref-name read-depth map-qual> [<ref-name read-depth map-qual> ...]
                        Filter vcf/bcf variant calling file based on reference name, read depth and mapping quality

Examples

• Apply a filter to your bam file, keeping reads that have: mapping quality (MAPQ) scores >=20, base quality Phred score >=30, percent identity between the reads and reference >=95%, and have a minimum read length of 100 bp:

python3 bioinformatic_formats_tool.py my_alignment_file_sorted.bam --bam-filter -mq 20 -rq 30 -p 95 -l 100 --output ./Output_dir
Selected parameters for bam filter:
reference: .*, mapping quality: 20, read quality: 30, read length: 100, %-identity: 95.0
Finished
File <my_alignment_file_sorted.bam_filtered.bam> was created

• Convert 2 paired-end fastq files to a single interleaved fastq file:

python3 bioinformatic_formats_tool.py ERS2665906_trimmed_R1.fastq ERS2665906_trimmed_R2.fastq --fastq-concat --output ./Output_dir
Finished
File <output_interleaved_R1_R2.fastq> was created

• Covert a bam alignment file to a single interleaved (forward-reverse) fastq file:

python3 bioinformatic_formats_tool.py my_alignment_file_sorted.bam --bamtofastq -o ./Output_dir
Finished
File <my_alignment_file_sorted.bam.fastq> was created