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PacificBiosciences · Mar 8, 2024 · 3987f61 · 3987f61
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diff --git a/docs/cli.md b/docs/cli.md
@@ -11,6 +11,9 @@
   unsorted VCF file (`<OUTPUT_PREFIX>.vcf.gz`) and unsorted BAM file with pieces
   of HiFi reads overlapping the repeats (`<OUTPUT_PREFIX>.spanning.bam`).
 - `--threads <THREADS>` Number of threads. Set to 1 by default.
+- `--karyotype <KARYOTYPE>` Sample karyotype (XX or XY). Set to XX by default.
+- `--sample-name <SAMPLE_NAME>` Sample name. If it is not provided, the sample name is extracted from the input BAM or file stem.
+- `--max-depth <MAX_DEPTH>` Maximum locus depth. Set to 250 by default.
 
 ## TRVZ command-line options
 

diff --git a/docs/vcf_files.md b/docs/vcf_files.md
@@ -39,7 +39,7 @@ the VCF file.
 |----------------|----------------------------------------------|---------------|
 | GT             | Genotype                                     | 1/2           |
 | AL             | Allele length in bps                         | 84,105        |
-| ALCI           | Confidence interval for HL                   | 80-85,102-114 |
+| ALLR           | Length range for AL                          | 80-85,102-114 |
 | SD             | Number of reads spanning each allele         | 28,18         |
 | MC             | Count of motifs of each TR on each allele    | 17_9,24_9     |
 | MS             | Span of each TR on each allele               | 0(0-51)_1(57-84),0(0-72)_1(78-105) |