Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls.

References:

• Pedersen BS, Quinlan AR. Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls. Gigascience. 2019 Apr 1;8(4):giz040. doi: 10.1093/gigascience/giz040. PMID: 31222198; PMCID: PMC6479422.

• DUPHOLD Main Site

• Module Name: duphold (see the modules page for more information)
• Multithreaded
• Environment variables set
  • DUPHOLD_HOME

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
[user@cn4338 ~]$ module load duphold
[+] Loading duphold  0.2.3  on cn4338 

Running help command:

[user@cn4338 data]$ duphold --help
version: 0.2.3

  Usage: duphold [options]

Options:
  -v --vcf            path to sorted SV VCF/BCF
  -b --bam            path to indexed BAM/CRAM
  -f --fasta          indexed fasta reference.
  -s --snp            optional path to snp/indel VCF/BCF with which to annotate SVs. BCF is highly recommended as it's much faster to parse.
  -t --threads         number of decompression threads. [default: 4]
  -o --output       output VCF/BCF (default is VCF to stdout) [default: -]
  -d --drop                 drop all samples from a multi-sample --vcf *except* the sample in --bam. useful for parallelization by sample followed by merge.
  -h --help                 show help

Annotate an SV:

[user@cn4338] cp -a /usr/local/apps/duphold/0.2.3/test_data .
[user@cn4338 test_data]$ duphold \
 --threads 4 \
 --vcf sparse_in.vcf \
 --bam sparse.cram \
 --fasta sparse.fa \
 --output output.bcf 
#To view output, load samtools and view with bcftools
[user@cn4338 test_data] module load samtools
[user@cn4338 test_data] bcftools view test-out.bcf
##fileformat=VCFv4.2
...
##bcftools_viewVersion=1.4-19-g1802ff3+htslib-1.4-29-g42bfe70
##bcftools_viewCommand=view CHM1_CHM13/full.37d5.vcf.gz; Date=Mon Sep 24 13:48:04 2018
...
##bcftools_viewVersion=1.17+htslib-1.17
##bcftools_viewCommand=view test-out.bcf; Date=Thu May 25 12:49:34 2023
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Eluc-CR2.F
NW_017858824.1  135118  72454   N       DEL   5875.46 .       SVTYPE=DEL;END=135332;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;GCF=0.306977  GT:DP:DHFC:DHFFC:DHBFC:DHSP     0/1:200:1.91667:0.597403:1.76923:0