running time

README.md

@@ -103,6 +103,26 @@ Hard filtration is applied, for GATK do not yet have the RNAseq training/truth r
 # GATK3, if you are using gatk4, please pay attention to the new arguments
 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 
 ```
+**one sample running time**
+
+Less than 4 hours
+
+Settings:
+
+- Disksize 500
+- Cluster OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc
+
+|     Module     |  Time   |
+| :------------: | :-----: |
+|    Mapping     | 1h20min |
+|    SamToBam    |   1h    |
+|    indexBam    |  5min   |
+|     Dedup      |  13min  |
+|   SplitReads   |  6min   |
+|      BQSR      |  21min  |
+|   Haplotyper   |  15min  |
+| Hardfiltration |  3min   |
+
 **Reference**
 
 1. GATK best practice https://software.broadinstitute.org/gatk/documentation/article.php?id=3891
@@ -110,4 +130,5 @@ java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg_19.fasta -V input.vcf
 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
+6. samtools manual http://www.htslib.org/doc/samtools.html
+