SAUNA paper - cfDNA Fragment dataset

SAUNA - Simulated Annealing for Unique Nucleosome Arrangements The dataset contains the data used in the publication of the SAUNA tool. 9 medium coverage (14-30x) cfDNA-sequencing files were mapped to the hg38 build of the human genome using bwa mem. Mapped sequence (Bam) files were converted into paired-end bed files using the `bedtools -pe` command. Consequently, the fragment information was extracted using the following commands. gunzip -c $file | awk 'BEGIN {OFS="\t"} $1 == $4 && ($6 - $2) <= 2000' | cut --output-delimiter=$'\t' -f1,2,6,8,9 | sort -k1,1V -k2,2n -k3,3n | bgzip > "${file%.sortByName.bed.gz}_hg38.frag.tsv.bgz" The resulting data files do not contain sequence information but can be converted back into bam files using Fragmentstein (https://github.com/uzh-dqbm-cmi/fragmentstein/, https://academic.oup.com/bioinformatics/article/40/1/btae017/7550024) and can be used for most analyses relevant in cfDNA-sequencing, with the exception of calling point mutations.