README.md

In xu-chang/patchwork-lite: Allele-specific Copy Number Analysis of whole genome data

patchwork-lite

Modified from the R package "Patchwork" on http://patchwork.r-forge.r-project.org/. patchwork-lite can read VCF results from newer versions of Samtools and BcfTools (Tested on v1.3 on both) without the need for mpileup files to lower the disk-space requirements.

• Compared to the original tool, I made change to patchwork.plot.r and patchwork.alleledata.r, added a python script mpile2alleles.py for reading VCF files.
• Rd documentation files are not changed.
• Only takes gz compressed vcf results as patchwork.plot() input , i.e. vcf.gz or vcf.bgz files.

Usage：

Prepare the VCF file like this:

samtools mpileup -t 'SP,INFO/AD,INFO/ADF,INFO/ADR' -uvf hg19.fa -r chr2:100000-110000 test.bam | \
  bcftools call --ploidy GRCh37 -mv | \
  bcftools filter -g 5 -G 5 -e 'TYPE!="snp" || AD[0]<5 || DP4[1]<2 || DP4[2]<2' -O z -o ./test.vcf.gz

so that we have only SNV lines and DP4 field is in the file.

And then run plot function like this:

patchwork.plot(Tumor_bam, Tumor_vcf_gz, Normal_bam, Normal_vcf_gz, Alpha=alpha, SD=sd)

Acknowledgements

Wenlong JIA ([e-mail])

xu-chang/patchwork-lite documentation built on May 26, 2019, 6:31 a.m.