Update README.md

README.md

@@ -48,8 +48,7 @@ than a reverse complement of the whole 600 bp construct.
 MPAC covers autosomes only; `from_pretrained` raises on chrX, chrY and anything else
 with no held-out fold.
 
-For allelic skew, pass matched reference and alternate contexts of 371 bp -- 180 bp
-upstream of the variant, the variant, 190 bp downstream. Each is tiled into eighteen
+For allelic skew, pass matched reference and alternate contexts. Each variant is tiled into eighteen
 200 bp windows at stride 10 and averaged, reproducing the scheme behind the
 published predictions.
 
@@ -58,9 +57,33 @@ out = ensemble.predict_skew(ref_contexts, alt_contexts, device="cuda")
 out["skew"]   # (n, 3), alt minus ref
 ```
 
-Command-line tooling for VCF-scale runs lives at
-[john-c-butts/MPAC](https://github.com/john-c-butts/MPAC).
-
+Command-line tools for MPAC can be found at:
+[Reilly-Lab-Yale/coda_mpac](https://github.com/Reilly-Lab-Yale/coda_mpac).
+
+Which provide greater control of prediction parameters including (but not limited to):
+  window number
+  step size
+  strand reduction
+  insert/full plasmid reverse complement
+  window aggregation (average, max, min, etc.)
+  
+An example prediction for SNVs from a VCF can be found in the methods of the publication and below:
+
+python vcf_predict.py --artifact_path {10X $MODEL} \ CHROMOSOME HOLDOUT MODELS TO ENSEMBLE
+--vcf_file ${VCF} \ VARIANTS OF INTEREST
+--fasta_file ${FASTA} \ REFERENCE GENOME
+--output ${OUTPUT} \ OUTPUT PATH
+--relative_start 9 \ START WINDOW
+--relative_end 180 \ END WINDOW
+--step_size 10 \ N WINDOWS
+--strand_reduction mean \ REDUCTION METHOD OF FWD/REV STRAND PREDICTIONS
+--window_reduction mean \ REDUCTION METHOD OF PREDICTION WINDOWS
+
+And include specialized prediction methods for:
+  small indels (<= 10bp recommended) (vcf_predict_indel.py)
+  haplotypes (vcf_predict_haplotype.py)
+
+Which can be run in the same way as vcf_predict.py but with modifications to handle sequence padding (vcf_predict_indel.py) or windowing (vcf_predict_haplotype.py)
 ## Citation
 
 ```bibtex