Move aou_recalibrate_gq_model_file and add acknkowledgement (#628)

README.md

@@ -5,6 +5,7 @@ A structural variation discovery pipeline for Illumina short-read whole-genome s
 ## Table of Contents
 * [Requirements](#requirements)
 * [Citation](#citation)
+* [Acknowledgements](#acknowledgements)
 * [Quickstart](#quickstart)
 * [Pipeline Overview](#overview)
     * [Cohort mode](#cohort-mode)
@@ -104,6 +105,14 @@ Additional references:
 [Werling et al. 2018. "An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder." Nature genetics 50.5, 727-736.](http://dx.doi.org/10.1038/s41588-018-0107-y)
 
 
+## <a name="acknowledgements">Acknowledgements</a>
+The following resources were produced using data from the All of Us Research Program and have been approved by the Program for public dissemination:
+
+* Genotype filtering model: "aou_recalibrate_gq_model_file" in "inputs/values/resources_hg38.json"
+
+The All of Us Research Program is supported by the National Institutes of Health, Office of the Director: Regional Medical Centers: 1 OT2 OD026549; 1 OT2 OD026554; 1 OT2 OD026557; 1 OT2 OD026556; 1 OT2 OD026550; 1 OT2 OD 026552; 1 OT2 OD026553; 1 OT2 OD026548; 1 OT2 OD026551; 1 OT2 OD026555; IAA #: AOD 16037; Federally Qualified Health Centers: HHSN 263201600085U; Data and Research Center: 5 U2C OD023196; Biobank: 1 U24 OD023121; The Participant Center: U24 OD023176; Participant Technology Systems Center: 1 U24 OD023163; Communications and Engagement: 3 OT2 OD023205; 3 OT2 OD023206; and Community Partners: 1 OT2 OD025277; 3 OT2 OD025315; 1 OT2 OD025337; 1 OT2 OD025276. In addition, the All of Us Research Program would not be possible without the partnership of its participants.
+
+
 ## <a name="quickstart">Quickstart</a>
 
 #### WDLs

inputs/values/resources_hg38.json

@@ -47,7 +47,7 @@
   "wgd_scoring_mask" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wgd_scoring_mask.hg38.gnomad_v3.bed",
   "wham_include_list_bed_file" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wham_whitelist.bed",
 
-  "aou_recalibrate_gq_model_file": "gs://gatk-sv-resources-secure/resources/recalibrator/gatk-sv-recalibrator.aou_phase_1.v1.model",
+  "aou_recalibrate_gq_model_file": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/gatk-sv-recalibrator.aou_phase_1.v1.model",
   "hgdp_recalibrate_gq_model_file": "gs://gatk-sv-hgdp/mw-sv-concordance-update/hgdp.gq_recalibrator.model",
   "recalibrate_gq_genome_tracks": [
     "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/ucsc-genome-tracks/hg38-RepeatMasker.bed.gz",