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@@ -68,7 +68,7 @@ choppy install huangyechao/wgs-germline |
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--fastq_1 测序数据的R1端 |
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--fastq_2 测序数据的R2端 |
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-K 10000000 该设置可用于比对过程中使得结果与线程数独立 |
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-o 比对结果输出的文件名 |
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-o 比对结果输出的文件名 |
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``` |
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**Dedup** |
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@@ -96,16 +96,16 @@ IS_METRIC_PDF the location and filename of the insertion size metrics report ou |
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**BQSR** |
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```bash |
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RECAL_DATA.TABLE the location and filename of the recalibration table |
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RECAL_DATA.TABLE.POST the location and filename of the temporary post recalibration table |
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RECAL_RESULT.CSV the location and filename of the temporary recalibration results output file used for plotting |
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RECAL_DATA.TABLE the location and filename of the recalibration table |
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RECAL_DATA.TABLE.POST the location and filename of the temporary post recalibration table |
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RECAL_RESULT.CSV the location and filename of the temporary recalibration results output file used for plotting |
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BQSR_PDF the location and filename of the BSQR results output file |
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``` |
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**Haplotyper** |
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```bash |
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VARIANT_VCF the location and filename of the variant calling output file |
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VARIANT_VCF the location and filename of the variant calling output file |
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``` |
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### APP输入 |