fix input

README.md

@@ -6,7 +6,7 @@
 
 **(1) Mapping to the reference genome (STAR)**
 
-Aligning RNAseq data to a reference genome is complicates by RNA splicing, [GATK RNAseq variant calling best practice](<https://software.broadinstitute.org/gatk/documentation/article.php?id=3891>) recommend [STAR](<https://github.com/alexdobin/STAR>).
+Aligning RNAseq data to a reference genome is complicates by RNA splicing, [GATK RNAseq variant calling best practice](<https://software.broadinstitute.org/gatk/documentation/article.php?id=3891>) recommends [STAR](<https://github.com/alexdobin/STAR>).
 
 Generate genome index files:
 
@@ -100,4 +100,10 @@ Hard filtration is applied, for GATK do not yet have the RNAseq training/truth r
 ```bash
 java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg_19.fasta -V input.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0" -filterName QD -filter "QD < 2.0" -o output.vcf 
 ```
-
+**Reference**
+1. GATK best practice https://software.broadinstitute.org/gatk/documentation/article.php?id=3891
+2. Sentieon manual https://support.sentieon.com/manual/RNA_call/rna/
+3. STAR github https://github.com/alexdobin/STAR
+4. Picard github https://github.com/broadinstitute/picard
+5. Picard manual https://broadinstitute.github.io/picard/
+6. samtools manual http://www.htslib.org/doc/samtools.html

inputs

@@ -13,9 +13,9 @@
   "{{ project_name }}.fastq_2": "{{ read2 }}",
   "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc' }}",
-  "{{ project_name }}.SAref_dir": "File",
+  "{{ project_name }}.SAref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/STAR_GRCh38/",
   "{{ project_name }}.SAMdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools",
-  "{{ project_name }}.STref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/STAR_GRCh38/",
+  "{{ project_name }}.STref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/",
   "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
   "{{ project_name }}.sample": "{{ sample }}",
   "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",