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smvplot

smvplot is a cmd line python tool to generate IGV-like screenshots.

Install

Install the package via pip

 pip install smvplot

Usage

$ smvplot --help
usage: smvplot [-h] --bam_paths STR --bam_names STR --ref FILE [--exclude_flag INT] [--map_quality INT] [--base_quality INT] [--max_depth_plot INT] [--vaf] [--vcf FILE] [--bed FILE]
               [--annotations FILE] [--prefix PREFIX] [--window N] [--samtoolsbin N] [--tabixbin N] [--plot_dir DIR] [--out_format STR]
               [region]

This script generates a png file for each entry in a vcf file, a bed file or a manually specified region.

positional arguments:
  region                syntax either 'chr:start-end' or 'chr:center', use --vcf or --bed for more convenience

optional arguments:
  -h, --help            show this help message and exit
  --bam_paths STR       input list of bam files separated by comma. Maximum 3 BAM files
  --bam_names STR       input list of names separated by comma. Same length as BAM files
  --ref FILE            input reference genome file (fastq format)
  --exclude_flag INT    Exclude the reads with corresponding SAM flags, [default = 3840]
  --map_quality INT     Minimum mapping quality for the reads, [default = 20]
  --base_quality INT    Minimum base quality for the variant, [default = 13]
  --max_depth_plot INT  Maximum read depth used to plot the high coverage region, [default = 500]
  --vaf                 Include the VAF of the central position in the plot title. Requires reference genome
  --vcf FILE            input vcf file ( as an alternative use --bed )
  --bed FILE            input bed file ( as an alternative use --vcf )
  --annotations FILE    annotation track indexed with tabix
  --prefix PREFIX       target directory and file name prefix for generated output files, [default = smvplot]
  --window N            the output file for position X will show the region [X-window,X+window], [default = 100]
  --samtoolsbin N       the path to the samtools binary, [default = samtools]
  --tabixbin N          the path to the tabix binary, [default = tabix]
  --plot_dir DIR        subfolder for the plots
  --out_format STR      Output format of the plot, [default = pdf]

Example plots

On the GIAB samples

  1. For a single variant from a single BAM
smvplot 
  --bam_paths HG001_merged.mdup.bam \
  --bam_names HG001 \
  --ref GRCh38_decoy_ebv_phiX_alt_hla_chr.fa \
  --plot_dir ~/smvplot_test \
  --prefix giab_HG001 \
  --out_format png
  chr1:3339544

  1. For a single variant from a TRIO (3 BAMs)
smvplot \
  --bam_paths HG002_merged.mdup.bam,HG003_merged.mdup.bam,HG004_merged.mdup.bam \
  --bam_names HG002_Son,HG003_Father,HG004_Mother \
  --ref GRCh38_decoy_ebv_phiX_alt_hla_chr.fa \
  --plot_dir ~/smvplot_test \
  --prefix giab_HG00234 \
  --out_format png \
  chr1:783175

  1. For multiple variants from a VCF/BED file
smvplot \
  --bam_paths HG002_merged.mdup.bam,HG003_merged.mdup.bam,HG004_merged.mdup.bam \
  --bam_names HG002_Son,HG003_Father,HG004_Mother \
  --ref GRCh38_decoy_ebv_phiX_alt_hla_chr.fa \
  --plot_dir ~/smvplot_test \
  --prefix giab_HG00234 \
  --out_format png \
  --vcf giab_benchmark_variants.vcf # --bed giab_benchmark_variants.vcf

Changelog

0.0.5

  • Patch: Update VAF calculation

0.0.4.14

  • Container generated via github actions and pushed to dockerhub

0.0.4

  • Added container

0.0.3.2

  • Minor bug fixes

0.0.3

  • Removed the underhand issue in the RNAseq histograms
  • Limit the VAF float decimals
  • In a multi-BAM settings, ignore the BAMs if the path does not exist

0.0.2

  • Add VAF to the title via pysamstats

0.0.1

  • Inital version upload to the PIP

Acknowledgements

The visualize.py was originally written for the DKFZ somatic indel workflow by Philip Ginsbach and Ivo Buchhalter. Here I have updated script to a python package and added a possibility of a third BAM and a RNAseq BAM file. And also generalized the BAM inputs.