ExpansionHunter Denovo (Custom)

ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs). EHdn is intended for analysis of a collection of BAM/CRAM files containing alignments of short (100-200bp) reads.

기존 EHdn v0.9와 다른 점

스크립트 추가 및 수정

1. list_TR.py

Tandem repeat 목록을 생성하는 스크립트

• Column info: Tandem repeat의 locus, motif, motif의 길이와 A,T nucleotide의 비율, Anchored IIRs에 대한 모든 샘플의 count의 합

• Usage

list_TR.py locus \
--multisample-profile multisample_profile.json \
--output TR_list.tsv \            
--min-count 2

2. outlier.py

• --min-count, --z-score, --no-ctrl option 추가 (locus 분석만 가능하고 motif 분석은 안됨)

  • --min-count: The minimum of depth-normalized count in at least one sample (Default: 2)

  • --z-score: The cutoff of z score (Default: 1)

  • --no-ctrl: If at least one control has z score higher than cutoff, skip.

• TSV 파일 형식 변환

  • counts column에서 count에 대한 sample id가 나오도록 변경

  • top_case_zscore column 대신 high_case_zscores column에 cutoff를 넘는 모든 sample의 id와 z score 표시

• Usage

outlier.py locus --manifest manifest.txt \
--multisample-profile multisample_profile.json \
--output outlier_locus.tsv \
--min-count 2 \
--z-score 10

3. hg19_to_hg38.py

• liftOver_path: The path of UCSC liftOver
• profile_list: List of EHdn STR profiles

License

ExpansionHunter Denovo is provided under the terms and conditions of the Apache License Version 2.0. It relies on several third party packages provided under other open-source licenses, please see COPYRIGHT.txt for additional details.