LUYAO REN
6 years ago
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README.md
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| # GATK3, if you are using gatk4, please pay attention to the new arguments | # 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 | 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** | **Reference** | ||||
| 1. GATK best practice https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 | 1. GATK best practice https://software.broadinstitute.org/gatk/documentation/article.php?id=3891 | ||||
| 3. STAR github https://github.com/alexdobin/STAR | 3. STAR github https://github.com/alexdobin/STAR | ||||
| 4. Picard github https://github.com/broadinstitute/picard | 4. Picard github https://github.com/broadinstitute/picard | ||||
| 5. Picard manual https://broadinstitute.github.io/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 | |||||
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