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mendelian_concordance
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LUYAO REN 5 lat temu
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7 zmienionych plików z 152 dodań i 69 usunięć
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  1. +33
    -33
      family.tsv
  2. +3
    -2
      inputs
  3. +2
    -1
      tasks/KeepVar.wdl
  4. +13
    -3
      tasks/mendelian.wdl
  5. +20
    -9
      tasks/merge.wdl
  6. +50
    -0
      tasks/sister.wdl
  7. +31
    -21
      workflow.wdl

+ 33
- 33
family.tsv Wyświetl plik

@@ -1,33 +1,33 @@
Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518_hc.vcf
Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530_hc.vcf
Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530_hc.vcf
Quartet_DNA_BGI_SEQ2000_WGE_LCL5_1_20190402 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_1_20190402_hc.vcf
Quartet_DNA_BGI_SEQ2000_WGE_LCL5_2_20190402 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_2_20190402_hc.vcf
Quartet_DNA_BGI_SEQ500_BGI_LCL5_1_20180328 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ500_BGI_LCL5_1_20180328_hc.vcf
Quartet_DNA_BGI_SEQ500_BGI_LCL5_2_20180328 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ500_BGI_LCL5_2_20180328_hc.vcf
Quartet_DNA_BGI_SEQ500_BGI_LCL5_3_20180328 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_BGI_SEQ500_BGI_LCL5_3_20180328_hc.vcf
Quartet_DNA_ILM_Nova_ARD_LCL5_1_20181108 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_1_20181108_RAW.vcf
Quartet_DNA_ILM_Nova_ARD_LCL5_2_20181108 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_2_20181108_RAW.vcf
Quartet_DNA_ILM_Nova_ARD_LCL5_3_20181108 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_3_20181108_RAW.vcf
Quartet_DNA_ILM_Nova_ARD_LCL5_4_20190111 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_4_20190111_RAW.vcf
Quartet_DNA_ILM_Nova_ARD_LCL5_5_20190111 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_5_20190111_RAW.vcf
Quartet_DNA_ILM_Nova_ARD_LCL5_6_20190111 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_ARD_LCL5_6_20190111_RAW.vcf
Quartet_DNA_ILM_Nova_BRG_LCL5_1_20171024 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_1_20171024_RAW.vcf
Quartet_DNA_ILM_Nova_BRG_LCL5_1_20180930 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_1_20180930_RAW.vcf
Quartet_DNA_ILM_Nova_BRG_LCL5_2_20180930 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_2_20180930_RAW.vcf
Quartet_DNA_ILM_Nova_BRG_LCL5_3_20180930 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_BRG_LCL5_3_20180930_RAW.vcf
Quartet_DNA_ILM_Nova_GAC_LCL5_1_20171025 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_GAC_LCL5_1_20171025_RAW.vcf
Quartet_DNA_ILM_Nova_NVG_LCL5_1_20171024 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_NVG_LCL5_1_20171024_RAW.vcf
Quartet_DNA_ILM_Nova_WUX_LCL5_1_20171024 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_Nova_WUX_LCL5_1_20171024_RAW.vcf
Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403_hc.vcf
Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403_hc.vcf
Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403_hc.vcf
Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329_RAW.vcf
Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329_RAW.vcf
Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329_RAW.vcf
Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216_RAW.vcf
Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216_RAW.vcf
Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216_RAW.vcf
Quartet_DNA_ILM_XTen_WUX_LCL5_4_20180703 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_4_20180703_RAW.vcf
Quartet_DNA_ILM_XTen_WUX_LCL5_5_20180703 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_5_20180703_RAW.vcf
Quartet_DNA_ILM_XTen_WUX_LCL5_6_20180703 oss://chinese-quartet/quartet-result-data/FDU/VCF/Quartet_DNA_ILM_XTen_WUX_LCL5_6_20180703_RAW.vcf
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL8_1_20180518.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL7_1_20180518.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL6_1_20180518.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL8_1_20180518.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL7_1_20180518.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL6_1_20180518.normed.callable.vcf.gz.tbi Quartet_DNA_BGI_SEQ2000_BGI_LCL8_1_20180518 Quartet_DNA_BGI_SEQ2000_BGI_LCL7_1_20180518 Quartet_DNA_BGI_SEQ2000_BGI_LCL5_1_20180518 BGI_SEQ2000_BGI_1
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL8_2_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL7_2_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL6_2_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL8_2_20180530.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL7_2_20180530.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL6_2_20180530.normed.callable.vcf.gz.tbi Quartet_DNA_BGI_SEQ2000_BGI_LCL8_2_20180530 Quartet_DNA_BGI_SEQ2000_BGI_LCL7_2_20180530 Quartet_DNA_BGI_SEQ2000_BGI_LCL5_2_20180530 BGI_SEQ2000_BGI_2
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL8_3_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL7_3_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL6_3_20180530.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL8_3_20180530.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL7_3_20180530.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_BGI_LCL6_3_20180530.normed.callable.vcf.gz.tbi Quartet_DNA_BGI_SEQ2000_BGI_LCL8_3_20180530 Quartet_DNA_BGI_SEQ2000_BGI_LCL7_3_20180530 Quartet_DNA_BGI_SEQ2000_BGI_LCL5_3_20180530 BGI_SEQ2000_BGI_3
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL8_1_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL7_1_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_1_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL6_1_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL8_1_20190402.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL7_1_20190402.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_1_20190402.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL6_1_20190402.normed.callable.vcf.gz.tbi Normal_DNA_M8 Normal_DNA_F7 Normal_DNA_D5 BGI_SEQ2000_WGE_1
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL8_2_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL7_2_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_2_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL6_2_20190402.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL8_2_20190402.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL7_2_20190402.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL5_2_20190402.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_BGI_SEQ2000_WGE_LCL6_2_20190402.normed.callable.vcf.gz.tbi PCRFree_DNA_M8 PCRFree_DNA_F7 PCRFree_DNA_D5 BGI_SEQ2000_WGE_2
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oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL8_1_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL7_1_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL6_1_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL8_1_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL7_1_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL6_1_20170403.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_ARD_LCL8_1_20170403 Quartet_DNA_ILM_XTen_ARD_LCL7_1_20170403 Quartet_DNA_ILM_XTen_ARD_LCL5_1_20170403 ILM_XTen_ARD_1
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL8_2_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL7_2_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL6_2_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL8_2_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL7_2_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL6_2_20170403.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_ARD_LCL8_2_20170403 Quartet_DNA_ILM_XTen_ARD_LCL7_2_20170403 Quartet_DNA_ILM_XTen_ARD_LCL5_2_20170403 ILM_XTen_ARD_2
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL8_3_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL7_3_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL6_3_20170403.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL8_3_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL7_3_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_ARD_LCL6_3_20170403.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_ARD_LCL8_3_20170403 Quartet_DNA_ILM_XTen_ARD_LCL7_3_20170403 Quartet_DNA_ILM_XTen_ARD_LCL5_3_20170403 ILM_XTen_ARD_3
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL8_1_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL7_1_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL6_1_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL8_1_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL7_1_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL6_1_20170329.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_NVG_LCL8_1_20170329 Quartet_DNA_ILM_XTen_NVG_LCL7_1_20170329 Quartet_DNA_ILM_XTen_NVG_LCL5_1_20170329 ILM_XTen_NVG_1
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL8_2_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL7_2_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL6_2_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL8_2_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL7_2_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL6_2_20170329.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_NVG_LCL8_2_20170329 Quartet_DNA_ILM_XTen_NVG_LCL7_2_20170329 Quartet_DNA_ILM_XTen_NVG_LCL5_2_20170329 ILM_XTen_NVG_2
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL8_3_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL7_3_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL6_3_20170329.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL8_3_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL7_3_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_NVG_LCL6_3_20170329.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_NVG_LCL8_3_20170329 Quartet_DNA_ILM_XTen_NVG_LCL7_3_20170329 Quartet_DNA_ILM_XTen_NVG_LCL5_3_20170329 ILM_XTen_NVG_3
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_1_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_1_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_1_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_1_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_1_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_1_20170216.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_WUX_LCL8_1_20170216 Quartet_DNA_ILM_XTen_WUX_LCL7_1_20170216 Quartet_DNA_ILM_XTen_WUX_LCL5_1_20170216 ILM_XTen_WUX_1
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_2_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_2_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_2_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_2_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_2_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_2_20170216.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_WUX_LCL8_2_20170216 Quartet_DNA_ILM_XTen_WUX_LCL7_2_20170216 Quartet_DNA_ILM_XTen_WUX_LCL5_2_20170216 ILM_XTen_WUX_2
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_3_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_3_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_3_20170216.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_3_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_3_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_3_20170216.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_WUX_LCL8_3_20170216 Quartet_DNA_ILM_XTen_WUX_LCL7_3_20170216 Quartet_DNA_ILM_XTen_WUX_LCL5_3_20170216 ILM_XTen_WUX_3
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_4_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_4_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_4_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_4_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_4_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_4_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_4_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_4_20180703.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_WUX_LCL8_4_20180703 Quartet_DNA_ILM_XTen_WUX_LCL7_4_20180703 Quartet_DNA_ILM_XTen_WUX_LCL5_4_20180703 ILM_XTen_WUX_4
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_5_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_5_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_5_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_5_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_5_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_5_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_5_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_5_20180703.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_WUX_LCL8_5_20180703 Quartet_DNA_ILM_XTen_WUX_LCL7_5_20180703 Quartet_DNA_ILM_XTen_WUX_LCL5_5_20180703 ILM_XTen_WUX_5
oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_6_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_6_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_6_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_6_20180703.normed.callable.vcf.gz oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL8_6_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL7_6_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL5_6_20180703.normed.callable.vcf.gz.tbi oss://pgx-result/renluyao/high_confidence_call/normed_vcf/Quartet_DNA_ILM_XTen_WUX_LCL6_6_20180703.normed.callable.vcf.gz.tbi Quartet_DNA_ILM_XTen_WUX_LCL8_6_20180703 Quartet_DNA_ILM_XTen_WUX_LCL7_6_20180703 Quartet_DNA_ILM_XTen_WUX_LCL5_6_20180703 ILM_XTen_WUX_6

+ 3
- 2
inputs Wyświetl plik

@@ -1,9 +1,10 @@
{
"{{ project_name }}.sister.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
"{{ project_name }}.mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
"{{ project_name }}.disk_size": "100",
"{{ project_name }}.merge.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
"{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
"{{ project_name }}.sdf": "oss://chinese-quartet/quartet-storage-data/reference_data/GRCh38.d1.vd1.sdf/",
"{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
"{{ project_name }}.KeepVar.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call:v1.0"
}
"{{ project_name }}.merge.sample_name": "{{ sample_name }}"
}

+ 2
- 1
tasks/KeepVar.wdl Wyświetl plik

@@ -23,4 +23,5 @@ task KeepVar {
File consistent_keeped_vcf = "consistent.all.selected.vcf"
File consistent_outlier_vcf = "consistent.all.selected_outlier.vcf"
}
}
}


+ 13
- 3
tasks/mendelian.wdl Wyświetl plik

@@ -15,7 +15,7 @@ task mendelian {
String disk_size
command <<<
rtg vcfmerge -o family.vcf.gz ${mother_vcf_gz} ${father_vcf_gz} ${child_vcf_gz}
rtg vcfmerge -o family.vcf.gz ${child_vcf_gz} ${mother_vcf_gz} ${father_vcf_gz}

rtg vcfannotate -i family.vcf.gz -o family.anno.vcf.gz \
--add-header "##SAMPLE=<ID=${mother_name},Sex=FEMALE>" \
@@ -35,9 +35,15 @@ task mendelian {
rtg bgzip ${family_name}.consistent.vcf
rtg index -f vcf ${family_name}.consistent.vcf.gz

rtg vcffilter -i ${child_vcf_gz} -o ${child_name}.violation.vcf.gz --include-vcf=${family_name}.violation.vcf.gz
zcat ${child_vcf_gz} | grep '##' > child_header
zcat ${family_name}.violation.vcf.gz | grep -v '##' | cut -f1-10 | awk '$10!~/\./' | cat header - > ${child_name}.violation.vcf
zcat ${family_name}.consistent.vcf.gz | grep -v '##' | cut -f1-10 | awk '$10!~/\./' | cat header - > ${child_name}.consistent.vcf

rtg vcffilter -i ${child_vcf_gz} -o ${child_name}.consistent.vcf.gz --include-vcf=${family_name}.violation.vcf.gz
rtg bgzip ${child_name}.violation.vcf
rtg index -f vcf ${child_name}.violation.vcf.gz

rtg bgzip ${child_name}.consistent.vcf
rtg index -f vcf ${child_name}.consistent.vcf.gz

>>>

@@ -50,6 +56,10 @@ task mendelian {
output {
File family_vcf_gz = "${family_name}.family.anno.mendelian.vcf.gz"
File family_vcf_index = "${family_name}.family.anno.mendelian.vcf.gz.tbi"
File family_violation_vcf_gz = "${family_name}.violation.vcf.gz"
File family_violation_vcf_idx = "${family_name}.violation.vcf.gz.tbi"
File family_consistent_vcf_gz = "${family_name}.consistent.vcf.gz"
File family_consistent_vcf_idx = "${family_name}.consistent.vcf.gz.tbi"
File violation_vcf_gz = "${child_name}.violation.vcf.gz"
File violation_vcf_idx = "${child_name}.violation.vcf.gz.tbi"
File consistent_vcf_gz = "${child_name}.consistent.vcf.gz"

+ 20
- 9
tasks/merge.wdl Wyświetl plik

@@ -1,15 +1,25 @@
task merge {
Array[File] violation_vcf_gz
Array[File] violation_vcf_idx
Array[File] consistent_vcf_gz
Array[File] consistent_vcf_idx
Array[File] child_violation_sister
Array[File] child_violation_sister_idx
Array[File] child_violation_nonsister
Array[File] child_violation_nonsister_idx
Array[File] child_consistent_sister
Array[File] child_consistent_sister_idx
Array[File] child_consistent_nonsister
Array[File] child_consistent_nonsister_idx
String sample_name
String docker
String cluster_config
String disk_size
command <<<
rtg vcfmerge --force-merge-all --no-gzip -o all.violation.vcf ${sep=" " violation_vcf_gz}
rtg vcfmerge --force-merge-all --no-gzip -o all.consistent.vcf ${sep=" " consistent_vcf_gz}
rtg vcfmerge --force-merge-all --no-gzip -o ${sample_name}.violation.sister.vcf ${sep=" " child_violation_sister}

rtg vcfmerge --force-merge-all --no-gzip -o ${sample_name}.violation.nonsister.vcf ${sep=" " child_violation_nonsister}

rtg vcfmerge --force-merge-all --no-gzip -o ${sample_name}.consistent.sister.vcf ${sep=" " child_consistent_sister}
rtg vcfmerge --force-merge-all --no-gzip -o ${sample_name}.consistent.nonsister.vcf ${sep=" " child_consistent_nonsister}
>>>

runtime {
@@ -19,8 +29,9 @@ task merge {
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File violation_merged_vcf = "all.violation.vcf"
File consistent_merged_vcf = "all.consistent.vcf"
File violation_sister_merged_vcf = "${sample_name}.violation.sister.vcf"
File violation_nonsister_merged_vcf = "${sample_name}.violation.nonsister.vcf"
File consistent_sister_merged_vcf = "${sample_name}.consistent.sister.vcf"
File consistent_nonsister_merged_vcf = "${sample_name}.consistent.nonsister.vcf"
}
}


+ 50
- 0
tasks/sister.wdl Wyświetl plik

@@ -0,0 +1,50 @@
task sister {
File violation_vcf_gz
File violation_vcf_idx
File consistent_vcf_gz
File consistent_vcf_idx
File sister_vcf_gz
File sister_vcf_idx
File sdf
String child_name
String docker
String cluster_config
String disk_size
command <<<
rtg vcfeval -b ${sister_vcf_gz} -c ${violation_vcf_gz} -o violation -t ${sdf}

rtg vcfeval -b ${sister_vcf_gz} -c ${consistent_vcf_gz} -o consistent -t ${sdf}

mv violation/tp.vcf.gz ${child_name}.violation.sister.vcf.gz
mv violation/fp.vcf.gz ${child_name}.violation.nonsister.vcf.gz
mv violation/tp.vcf.gz.tbi ${child_name}.violation.sister.vcf.gz.tbi
mv violation/fp.vcf.gz.tbi ${child_name}.violation.nonsister.vcf.gz.tbi
mv violation/summary.txt ${child_name}.violation.summary.txt

mv consistent/tp.vcf.gz ${child_name}.consistent.sister.vcf.gz
mv consistent/fp.vcf.gz ${child_name}.consistent.nonsister.vcf.gz
mv consistent/tp.vcf.gz.tbi ${child_name}.consistent.sister.vcf.gz.tbi
mv consistent/fp.vcf.gz.tbi ${child_name}.consistent.nonsister.vcf.gz.tbi
mv consistent/summary.txt ${child_name}.consistent.summary.txt
>>>

runtime {
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File child_violation_sister = "${child_name}.violation.sister.vcf.gz"
File child_violation_sister_idx = "${child_name}.violation.sister.vcf.gz.tbi"
File child_violation_nonsister = "${child_name}.violation.nonsister.vcf.gz"
File child_violation_nonsister_idx = "${child_name}.violation.nonsister.vcf.gz.tbi"
File child_consistent_sister = "${child_name}.consistent.sister.vcf.gz"
File child_consistent_sister_idx = "${child_name}.consistent.sister.vcf.gz.tbi"
File child_consistent_nonsister = "${child_name}.consistent.nonsister.vcf.gz"
File child_consistent_nonsister_idx = "${child_name}.consistent.nonsister.vcf.gz.tbi"
File violation_summary = "${child_name}.violation.summary.txt"
File consistent_summary = "${child_name}.consistent.summary.txt"
}
}

+ 31
- 21
workflow.wdl Wyświetl plik

@@ -1,6 +1,6 @@
import "./tasks/mendelian.wdl" as mendelian
import "./tasks/sister.wdl" as sister
import "./tasks/merge.wdl" as merge
import "./tasks/KeepVar.wdl" as KeepVar
workflow {{ project_name }} {
File inputSamplesFile
@@ -15,35 +15,45 @@ workflow {{ project_name }} {
mother_vcf_gz=sample[0],
father_vcf_gz=sample[1],
child_vcf_gz=sample[2],
mother_vcf_idx=sample[3],
father_vcf_idx=sample[4],
child_vcf_idx=sample[5],
mother_name=sample[6],
father_name=sample[7],
child_name=sample[8],
family_name=sample[9],
mother_vcf_idx=sample[4],
father_vcf_idx=sample[5],
child_vcf_idx=sample[6],
mother_name=sample[8],
father_name=sample[9],
child_name=sample[10],
family_name=sample[11],
sdf=sdf,
cluster_config=cluster_config,
disk_size=disk_size
}
}

call merge.merge as merge {
input:
violation_vcf_gz=mendelian.violation_vcf_gz,
violation_vcf_idx=mendelian.violation_vcf_idx,
consistent_vcf_gz=mendelian.consistent_vcf_gz,
consistent_vcf_idx=mendelian.consistent_vcf_idx,
cluster_config=cluster_config,
disk_size=disk_size
call sister.sister as sister {
input:
violation_vcf_gz=mendelian.violation_vcf_gz,
violation_vcf_idx=mendelian.violation_vcf_idx,
consistent_vcf_gz=mendelian.consistent_vcf_gz,
consistent_vcf_idx=mendelian.consistent_vcf_idx,
sister_vcf_gz=sample[3],
sister_vcf_idx=sample[7],
sdf=sdf,
child_name=sample[10],
cluster_config=cluster_config,
disk_size=disk_size
}

}

call KeepVar.KeepVar as KeepVar {
call merge.merge as merge {
input:
violation_merged_vcf=merge.violation_merged_vcf,
consistent_merged_vcf=merge.consistent_merged_vcf,
child_violation_sister=sister.child_violation_sister,
child_violation_sister_idx=sister.child_violation_sister_idx,
child_violation_nonsister=sister.child_violation_nonsister,
child_violation_nonsister_idx=sister.child_violation_nonsister_idx,
child_consistent_sister=sister.child_consistent_sister,
child_consistent_sister_idx=sister.child_consistent_sister_idx,
child_consistent_nonsister=sister.child_consistent_nonsister,
child_consistent_nonsister_idx=sister.child_consistent_nonsister_idx,
cluster_config=cluster_config,
disk_size=disk_size
}

}

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