CrossMap

hg19 <-> hg38 변환이 필요한 경우에 유용한 프로그램이다.

 

- Homepage : http://crossmap.sourceforge.net/

- Github : https://github.com/liguowang/CrossMap

$ pip3 install pyBigWig
$ conda install pybigwig -c conda-forge -c bioconda
# https://github.com/deeptools/pyBigWig

$ pip3 install CrossMap

 

기본적인 사용방법

$ CrossMap.py bed <chain_file> <input.bed> <output.bed>

$ CrossMap.py

Program: CrossMap (v0.5.2)

Description:
  CrossMap is a program to convert genome coordinates between different reference
  assemblies(e.g. from human hg19 to hg38 or vice versa). The supported file
  formats include BAM, BED, BigWig, CRAM, GFF, GTF, GVCF, MAF (mutation annotation
  format), SAM, Wiggle, and VCF.

Usage: CrossMap.py <command> [options]

        bam    convert BAM, CRAM or SAM format file.
        bed    convert BED, bedGraph or other BED-like files.
        bigwig convert BigWig file.
        gff    convert GFF or GTF format file.
        gvcf   convert GVCF file.
        maf    convert MAF (mutation annotation format) file.
        region convert big genomic regions (in BED format) such as CNV blocks.
        vcf    convert VCF file.
        wig    convert Wiggle or bedGraph format file.

 

BED file

- https://github.com/mobidic/BARMEN/find/master

- https://github.com/AstraZeneca-NGS/reference_data

 

Chain

- http://hgdownload.cse.ucsc.edu/gbdb/hg19/liftOver/

- http://hgdownload.cse.ucsc.edu/gbdb/hg38/liftOver/