text updates for PIE

docs/pecan/pie-faq/index.md

@@ -6,18 +6,12 @@ These details are for use by our clinical analysts for variant classification an
 
 **Q: Are there limits on the size of VCF files?**
 
-Uploaded files must not exceed 4 gigabytes. If an uploaded file is larger
-than 2 megabytes, the cancer predisposition gene list filter will be
+Uploaded files must not exceed 2 MB. If an uploaded file is larger
+than 2 MB, the cancer predisposition gene list filter will be
 automatically enabled unless you are using a custom gene list. This reduces
 the processing burden on the system by removing variants outside of targeted
-genes.
+genes. You can archive the file in a .gz or .bgz if needed.
 
-**Q: Is there an example/demo VCF I can try with PIE?**
-
-A. You can use [this VCF](ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz)
-from the Genome in a Bottle project. This ~133 megabyte
-bgzip-compressed VCF was used during testing of Pecan PIE and is known
-to work. These variants are mapped to GRCh37.
 
 **Q. What genome versions are supported?**
 

docs/pecan/use-cases/index.md

@@ -4,12 +4,12 @@ title: Common Use Cases
 
 The following are common scenarios a user might want to achieve in PeCan. 
 
-1. The [homepage](https://pecan-v2.staging.stjude.cloud/) is designed to familiarize the user with the components of the platform along with key features found in each. Additionally, the user can explore our [Help Guides](https://university.stjude.cloud/docs/pecan/) which allows the user to read more about each data facet, including the [data and methods](./methods-data) to generate each facet. 
-2. A user can navgiate to [PIE](https://pecan-v2.staging.stjude.cloud/pie) and once signed in, the user can [submit a job](https://pecan-v2.staging.stjude.cloud/pie/submit-job) which allows the upload of a VCF file or the ability to enter a single variant. **Read more information about PIE [here](./pecan-pie).**
-3. On the [histology](https://pecan-v2.staging.stjude.cloud/histology) data facet, a user can search on the advanced search page so a specific CompBioID. This does not populate approximates but a user can search partial IDs. **Read more about [Histology here](https://university.stjude.cloud/docs/pecan/histology).**
-4. On the [histology](https://pecan-v2.staging.stjude.cloud/histology) data facet, a user can select a histology image and then navigate to the `Open Viewer` whereby the user can expect the histology image using the OpenSeaDragon features. **Read more about [Histology here].**
-5. On the [histology](https://pecan-v2.staging.stjude.cloud/histology) data facet, a user can select a histology image and then access the relevant clinical notes per slide. 
-6. On the [histology](https://pecan-v2.staging.stjude.cloud/histology) data facet, a user can select a histology image and copy the URL to share with others and/or download the image for personal use. These two features can also be accessed on the Open Viewer page. **Read more about [Histology here](https://university.stjude.cloud/docs/pecan/histology).**
+1. The [homepage](https://pecan.stjude.cloud/) is designed to familiarize the user with the components of the platform along with key features found in each. Additionally, the user can explore our [Help Guides](https://university.stjude.cloud/docs/pecan/) which allows the user to read more about each data facet, including the [data and methods](./methods-data) to generate each facet. 
+2. A user can navgiate to [PIE](https://pecan.stjude.cloud/pie) and once signed in, the user can [submit a job](https://pecan-v2.staging.stjude.cloud/pie/submit-job) which allows the upload of a VCF file or the ability to enter a single variant. **Read more information about PIE [here](./pecan-pie).**
+3. On the [histology](https://pecan.stjude.cloud/histology) data facet, a user can search on the advanced search page so a specific CompBioID. This does not populate approximates but a user can search partial IDs. **Read more about [Histology here](https://university.stjude.cloud/docs/pecan/histology).**
+4. On the [histology](https://pecan.stjude.cloud/histology) data facet, a user can select a histology image and then navigate to the `Open Viewer` whereby the user can expect the histology image using the OpenSeaDragon features. **Read more about [Histology here].**
+5. On the [histology](https://pecan.stjude.cloud/histology) data facet, a user can select a histology image and then access the relevant clinical notes per slide. 
+6. On the [histology](https://pecan.stjude.cloud/histology) data facet, a user can select a histology image and copy the URL to share with others and/or download the image for personal use. These two features can also be accessed on the Open Viewer page. **Read more about [Histology here](https://university.stjude.cloud/docs/pecan/histology).**
 7. On the Sunburst, the user can select a disease and/or subtype which then updates the patient and sample stat summary in the top left. Available samples will also update accordingly per data facet. **Read more on [Getting Started here](https://university.stjude.cloud/docs/pecan/).**
 8. The user can search a gene which takes them to the ProteinPaint view in the Variants data facet. Here, no filtering will be precomputed and the `Pedatric` dataset for hg38 will be defaulted. The user can navigate to the Variants data facet and click on ProteinPaint. The default view will be for TP53 with hg38 genome. The user can filter by diagnosis and/or subtype or move coordinates by typing a new gene in the width container. **Read more about [Variants:ProteinPaint here](https://university.stjude.cloud/docs/pecan/variants).**
 9.  The user can search a variant which takes them to the Variant Details page in the Variants data facet. Here, the variant information will be deafulted to hg19. The user can navigate to the Variants data facet and click on ProteinPaint. The default view will be for TP53 with hg38 genome. The user can filter by diagnosis and/or subtype or move coordinates by typing a new gene in the width container. The user can find a Variant Details page two ways: