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quickstart.md

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Quickstart

hificnv \
    --bam {BAM} \
    --ref {REF_FASTA} \
    --exclude {EXCLUDE} \
    --expected-cn {EXPECTED_CN} \
    --threads {THREADS} \
    --output-prefix {OUTPUT_PREFIX}

Parameters:

  • {BAM} - a BAM file containing reads from the sample
  • {REF_FASTA} - a FASTA file containing the reference genome, gzip allowed
  • {EXCLUDE} - a BED file of excluded regions, recommended for hg38: cnv.excluded_regions.common_50.hg38.bed.gz
  • {EXPECTED_CNV} - a BED file containing regions with deviant copy number expectations (two copy is the default if unspecified), male and female expectation files are proved in the expected_cn folder
  • {THREADS} - number of threads to use
  • {OUTPUT_PREFIX} - the prefix for all output files

Auxiliary data files

See auxiliary file generation for details on the above recommended data files.

Example

Example of running HiFiCNV on an HG002 (male) WGS sample. An optional VCF file is provided for minor-allele frequency outputs in this example:

$ hificnv \
>     --bam /path/to/HG002.GRCh38.deepvariant.haplotagged.bam \
>     --maf /path/to/HG002.GRCh38.deepvariant.phased.vcf.gz \
>     --ref /path/to/human_GRCh38_no_alt_analysis_set.fasta \
>     --exclude /path/to/common_events.exclude-merged.bed.gz \
>     --expected-cn /path/to/male_ecn.bed \
>     --threads 8 \
>     --output-prefix HG002_male
[2022-09-29][06:22:57][hificnv][INFO] Starting hificnv
[2022-09-29][06:22:57][hificnv][INFO] cmdline: hificnv --bam /path/to/HG002.GRCh38.deepvariant.haplotagged.bam --ref /path/to/human_GRCh38_no_alt_analysis_set.fasta --exclude /path/to/common_events.exclude-merged.bed.gz --expected-cn /path/to/male_ecn.bed --threads 8 --output-prefix HG002_male
[2022-09-29][06:22:57][hificnv][INFO] Running on 8 threads
[2022-09-29][06:22:57][hificnv][INFO] Reading reference genome from file '/path/to/human_GRCh38_no_alt_analysis_set.fasta'
[2022-09-29][06:23:29][hificnv][INFO] Reading excluded regions from file '/path/to/common_events.exclude-merged.bed.gz'
[2022-09-29][06:23:29][hificnv][INFO] Reading expected CN regions from file '/path/to/male_ecn.bed'
[2022-09-29][06:23:29][hificnv][INFO] Processing alignment file '/path/to/HG002.GRCh38.deepvariant.haplotagged.bam'
[2022-09-29][06:37:47][hificnv][INFO] Writing depth track to bigwig file: 'HG002_male.HG002.depth.bw'
[2022-09-29][06:37:48][hificnv][INFO] Scanning minor allele frequency data from file '/path/to/HG002.GRCh38.deepvariant.phased.vcf.gz'
[2022-09-29][06:38:01][hificnv][INFO] Writing bigwig maf track to file: 'HG002_male.HG002.maf.bw'
[2022-09-29][06:38:18][hificnv][INFO] Segmenting copy number
[2022-09-29][06:38:18][hificnv][INFO] Haploid coverage estimates for sample 'HG002', iteration 1. Uncorrected: 14.955 GC-Corrected: 15.708
[2022-09-29][06:38:21][hificnv][INFO] Haploid coverage estimates for sample 'HG002', iteration 2. Uncorrected: 14.955 GC-Corrected: 15.708
[2022-09-29][06:38:23][hificnv][INFO] Writing bedgraph copy number track to file: 'HG002_male.HG002.copynum.bedgraph'
[2022-09-29][06:38:23][hificnv][INFO] Writing copy number variants to file: 'HG002_male.HG002.vcf.gz'
[2022-09-29][06:38:23][hificnv][INFO] hificnv completed. Total Runtime: 00:15:26.323
$ ls
HG002_male.HG002.copynum.bedgraph  HG002_male.HG002.depth.bw  HG002_male.HG002.maf.bw  HG002_male.HG002.vcf.gz  HG002_male.log

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