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Sorts indels into mutational classes

Project description

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:

To install, use pip:

pip install sorting_hat

Example run

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


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:

Allison Seiden <>

Project details

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