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README.md

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-# kf-jointgenotyping-workflow
+# Kids First DRC Joint Genotyping Workflow
+
+![data service logo](https://github.com/d3b-center/d3b-research-workflows/raw/master/doc/kfdrc-logo-sm.png)
+
+Kids First Data Resource Center Joint Genotyping Workflow (cram-to-deNovoGVCF). Cohort sample variant calling and genotype refinement.
+
+Using existing gVCFs, likely from GATK Haplotype Caller, we follow this workflow: [Germline short variant discovery (SNPs + Indels)](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145), to create family joint calling and joint trios (typically mother-father-child) variant calls. Peddy is run to raise any potential issues in family relation definitions and sex assignment.
+
+
+### Tips To Run:
+
+1. inputs vcf files are the gVCF files from GATK Haplotype Caller, need to have the index **.tbi** files copy to the same project too.
+
+2. ped file in the input shows the family relationship between samples, the format should be the same as in GATK website [link](https://gatkforums.broadinstitute.org/gatk/discussion/7696/pedigree-ped-files), the Individual ID, Paternal ID and Maternal ID must be the same as in the inputs vcf files header.
+
+3. Here we recommend to use GRCh38 as reference genome to do the analysis, positions in gVCF should be GRCh38 too.
+
+4. Reference locations:
+    - https://console.cloud.google.com/storage/browser/broad-references/hg38/v0/
+    - kfdrc bucket: s3://kids-first-seq-data/broad-references/
+    - cavatica: https://cavatica.sbgenomics.com/u/yuankun/kf-reference/
+5. Suggested inputs:
+    -  Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz
+    -  Homo_sapiens_assembly38.dbsnp138.vcf
+    -  hapmap_3.3.hg38.vcf.gz
+    -  Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
+    -  1000G_omni2.5.hg38.vcf.gz
+    -  1000G_phase1.snps.high_confidence.hg38.vcf.gz
+    -  Homo_sapiens_assembly38.dict
+    -  Homo_sapiens_assembly38.fasta.fai
+    -  Homo_sapiens_assembly38.fasta
+    -  1000G_phase3_v4_20130502.sites.hg38.vcf
+    -  hg38.even.handcurated.20k.intervals
+    -  homo_sapiens_vep_93_GRCh38_convert_cache.tar.gz, from ftp://ftp.ensembl.org/pub/release-93/variation/indexed_vep_cache/ - variant effect predictor cache.
+    -  wgs_evaluation_regions.hg38.interval_list
+
 ## basic info
-- pipeline flowchart:
-  - [draw.io](https://tinyurl.com/y9cq6yp8)
+![pipeline flowchart](./docs/kf_jointgenotyping_workflow_optimized_and_refinement.cwl.png)
 - tool images: https://hub.docker.com/r/kfdrc/
 - dockerfiles: https://github.com/d3b-center/bixtools