refactor(heteroplasmy): parse mutserve .txt table instead of VCF (smoke-validated)
Smoke-test (b41/run07) confirmed the caller: mutserve 2.0.3 accepts the module's flags, MT.fa works as --reference (no --contig-name), AF is in FORMAT, and heteroplasmy was detected (pos 204/2814/11762/16189). The 'AF not found' in the smoke was an artifact of querying the plain-gzip VCF directly (mutserve writes .vcf.gz as plain gzip; bcftools needs the norm -Oz re-block). PARSE_HETEROPLASMY now reads the mutserve variant table (${id}_${arm}.txt) with awk: it carries per-strand coverage (the §5e control) + explicit Type/Filter, is richer than the VCF, and sidesteps the bgzip issue. The normalized VCF is kept only for Haplocheck. MUTSERVE now emits the .txt; PARSE drops the mtdnaserver container (awk on the main image); the master TSV gains pos/variant_level/coverage/cov_fwd/cov_rev/type. Docs updated with validation status.
Loading
Please register or sign in to comment