Matiq
5385f76447
- flag C>T/G>A at read ends (end<=10) as FFPE-suspect, strand bias as supporting evidence - outputs: candidate_variants.tsv [is_ffpe_suspect,ffpe_reason], clean_variants.tsv, ffpe_suspect_variants.tsv, candidate_CtoT/GtoA_clean.bed - optional --vcf: produce .clean.vcf (without damaged) and .ffpe_flagged.vcf; with --keep-damaged mark FILTER=FFPE instead of removing - auto-create BAM/FASTA index if missing, improved error messages
17 lines
134 B
Plaintext
17 lines
134 B
Plaintext
.venv/
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__pycache__/
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*.pyc
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test_data/
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FFPE_QC/
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FFPE_sample/
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*.bam
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*.bai
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*.fai
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hg38.fa
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hg38.fa.gz
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*.vcf.gz
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*.tbi
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*.zip
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README.html
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124/
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