PughLab CompareFragmentSize (version 0.0.14)

This package can be used to compare fragment size of variant- and reference-allele containing reads in a plasma cfDNA BAM file in order to classify variants as somatic (tend to have shorter fragments) or non-somatic (germline if VAF > 38%, CHIP or sequence artefacts). These functions are adapted from Vessies et al. (2022).

Installation

devtools::install_github("pughlab/CompareFragmentSize")

Dependencies

This package utilizes functions from the following packages:

• GenomicRanges
• GenomicAlignments
• BSgenome.Hsapiens.UCSC.hg38 (BSgenome.Hsapiens.UCSC.hg19)
• Rsamtools
• Biostrings
• ggplot2

Input Files

Target variants can be input in either MAF or TSV format. MAF format must contain these fields: Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele2, Tumor_Sample_Barcode (and optionally Variant_Type, Hugo_Symbol and HGVSc). TSV format must contain these fields: Chromosome, Start, End, REF, ALT, Sample (and optionally Variant_Type, Hugo_Symbol and HGVSc).

Sample	Chromosome	Start	End	REF	ALT
SMID1	chr1	1234456	1234456	A	T
SMID1	chr14	9872683	9872686	-	ATCG
SMID2	chr13	57244668	57244671	ATCG	-

RUN example

The included compareVariantFragmentSizes.R can be used to run all target variants for a single sample:

Rscript compareVariantFragmentSizes.R -b /path/to/sample.bam -o /path/to/output/directory -s Sample1 -t /path/to/targets.maf -g hg38

Sample	Hugo_Symbol	Chromosome	Start	End	Variant_Type	REF	ALT	HGVSc	Count_WT	Median_WT	Count_VAR	Median_VAR	KS.p	VAF	Classification	WTFS	VFS	ttest.p
Sample1	FANCD2	chr3	10088239	10088239	SNP	G	A	c.1135-25G>A	2260	167	372	164	8x10^-8	0.14	somatic	-1.23	-0.16	8x10^-8