docs: Add section on detecting coverage dropouts and interpreting dropout columns in TRGT documentation

Author: williamrowell

docs/trgt.md

@@ -11,3 +11,26 @@ chr4    39348424        39348483        ID=CANVAS_RFC1;MOTIFS=AAGGG,ACAGG,AGGGC,
 chr9    69037270        69037304        ID=FRDA_FXN;MOTIFS=A,GAA;STRUC=<TR>;INCLUDE_FAIL_READS
 chr13   102161574       102161726       ID=SCA27B_FGF14;MOTIFS=GAA,GAAGGA,GAAGAAGAAGAAGCA,AAGGAG;STRUC=<TR>;INCLUDE_FAIL_READS
 ```
+
+## Detecting coverage dropouts
+
+Dropouts in coverage at TRGT catalog loci may indicate the presence of large expansions that are not fully spanned by HiFi reads.  To detect such dropouts, we run a script (`find_trgt_dropouts.py`) after TRGT genotyping to compares the observed coverage at each locus with a fixed threshold (2 reads per expected haplotype) and reports abnormal coverage in `*.trgt.dropouts.txt`.  The columns in this file are as follows:
+
+- chrom
+- start
+- end
+- trid
+- expected_ploidy
+- hap1_count
+- hap2_count
+- unphased_count
+- fail_read_count
+- dropout (FullDropout, HaplotypeDropout, PhasingDropout)
+
+The `fail_read_count` column indicates the number of `fail_reads` that aligned to the locus.  This can help interpret dropouts at loci where `fail_reads` were included for genotyping.
+
+The dropout column can be interpreted as follows:
+
+- FullDropout: total HiFi read count (hap1 + hap2 + unphased) is less than `expected_ploidy * 2`
+- HaplotypeDropout: one expected haplotype has fewer than 2 HiFi reads
+- PhasingDropout: the total HiFi read depth is at least `expected_ploidy * 2`, but both haplotypes have fewer than 2 reads