Frequently Used commands - abyzovlab/CNVpytor GitHub Wiki

Available reference genome names: rg_info

Usage: cnvpytor -rg_info (currently available for development version)

Example output: 
Available reference genomes:
* hg19
	Name: GRCh37
	Species: human
	Chromosomes: 25
	GC file specified: Yes
	Mask file specified: Yes
	Ensembl API link specified: Yes
* hg38
	Name: GRCh38
	Species: human
	Chromosomes: 25
	GC file specified: Yes
	Mask file specified: Yes
	Ensembl API link specified: Yes
* chm13
	Name: CHM13 v2.0
	Species: human
	Chromosomes: 25
	GC file specified: Yes
	Mask file specified: Not
	Ensembl API link specified: Not
* chm13v1.1
	Name: CHM13 v1.1 + hg38 chrY
	Species: human
	Chromosomes: 25
	GC file specified: Yes
	Mask file specified: Not
	Ensembl API link specified: Not
* kn99
	Name: Cryptococcus neoformans var. grubii KN99 GCA_002216725.1
	Species: cryptococcus neoformans
	Chromosomes: 15
	GC file specified: Yes
	Mask file specified: Not
	Ensembl API link specified: Not

To view the contents of a pytor file: ls

Usage: cnvpytor -root file.pytor -ls

Example output:

If both rd and snps data are present.

Filename 'NA12877.pytor'
------------------------
File created: 2020-07-21 23:11 using CNVpytor ver 1.0

Chromosomes with RD signal: chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY

Chromosomes with SNP signal: chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY

Using reference genome: hg19 [ GC: yes, mask: yes ]

Chromosomes with RD histograms [bin sizes]: chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr1, chr20, chr21, chr22, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY [100000]

Chromosomes with SNP histograms [bin sizes]: chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr1, chr20, chr21, chr22, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrX, chrY [100000]

Chromosome lengths: {'chrM': '16571', 'chr1': '249250621', 'chr2': '243199373', 'chr3': '198022430', 'chr4': '191154276', 'chr5': '180915260', 'chr6': '171115067', 'chr7': '159138663', 'chr8': '146364022', 'chr9': '141213431', 'chr10': '135534747', 'chr11': '135006516', 'chr12': '133851895', 'chr13': '115169878', 'chr14': '107349540', 'chr15': '102531392', 'chr16': '90354753', 'chr17': '81195210', 'chr18': '78077248', 'chr19': '59128983', 'chr20': '63025520', 'chr21': '48129895', 'chr22': '51304566', 'chrX': '155270560', 'chrY': '59373566'}

if any of the data is missing than that column will be empty.

Chromosomes with SNP histograms [bin sizes]:  []
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