Sorting Hat

Sorts indels into classes defined as follows:

• homopolymer run (HR): mutation is in a region where there are 6 or more copies of the nucleotide being inserted or deleted

• change in copy count (CCC): the allele being inserted or deleted has 1 or more repeats in the mutation region

• no change in copy count (non-CCC): the allele being inserted or deleted is not repeated in the mutation region

In order to use sorting_hat, you must ensure the following are installed:

• Python >=3.5.0

• bedtools >=2.27.0

To install, use pip:

pip install sorting_hat

Example run

sorting_hat --bed test.bed \
            --fasta test.fasta \
            --repeat repeat_masker.txt

Usage

sorting_hat [-h] -b BED -f FASTA -r REPEAT [-o OUTPUT]

Sorts indels into mutational classes

-b BED, --bed BED

Location of BED file with all variants. Must be formatted as Chrom/Start/End/Ref/Alt/PatientID.

-f FASTA, --fasta FASTA

Location of reference fasta file.

-r REPEAT, --repeat REPEAT

Location of RepeatMasker file downloaded from UCSC Genome Browser. Refer to docs to see how to download RepeatMasker.

-o OUTPUT, --output OUTPUT

Name of output file, if not chosen then will print to stdout.

To download RepeatMasker from UCSC Genome Browser, see photos in ‘data’ folder on github: https://github.com/allisonseiden/sorting_hat

Allison Seiden <ahseiden@gmail.com>