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chromosome start end gene log2 depth weight | |
chr1 15669 15990 WASH7P 0.134313 45.86 0.589343 | |
chr1 24680 24915 WASH7P 0.410313 91.55 0.147485 | |
chr1 29226 29428 WASH7P -0.557187 15.59 0.500307 | |
chr1 35626 35828 FAM138A 0.957813 113.79 0.506535 | |
chr1 62981 63221 OR4G11P 1.14781 239.14 0.384789 | |
chr1 63221 63462 OR4G11P 0.821813 173.77 0.418936 | |
chr1 69283 69532 OR4F5 0.608312 146.73 0.387104 | |
chr1 258985 259187 AP006222.2 1.30581 385.4 0.158045 | |
chr1 326406 326768 RP4-669L17.10,RP4-669L17.8 1.25731 103.33 0.505529 |
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##fileformat=VCFv4.2 | |
##FILTER=<ID=PASS,Description="All filters passed"> | |
##FILTER=<ID=alt_allele_in_normal,Description="Evidence seen in the normal sample"> | |
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor"> | |
##FILTER=<ID=clustered_read_position,Description="Evidence for somatic variant clusters near the ends of reads"> | |
##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic"> | |
##FILTER=<ID=homologous_mapping_event,Description="More than three events were observed in the tumor"> | |
##FILTER=<ID=multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal"> | |
##FILTER=<ID=panel_of_normals,Description="Seen in at least 2 samples in the panel of normals"> | |
##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region"> |
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chromosome start end gene log2 depth probes weight | |
chr1 15669 874867 WASH7P,FAM138A,OR4G11P,OR4F5,AP006222.2,RP4-669L17.10,RP4-669L17.8,AL732372.1,RP4-669L17.10,RP4-669L17.2,RP5-857K21.15,WBP1LP7,MTND1P23,MTND2P28,RP5-857K21.1,RP5-857K21.2,RP5-857K21.3,RP5-857K21.4,RP5-857K21.5,RP5-857K21.4,RP11-206L10.1,RP11-206L10.2,RP11-206L10.9,RP11-206L10.10,RP11-206L10.8,RP11-206L10.9,LINC00115,SAMD11,AL645608.1,SAMD11 0.477296 92.377 32 12.4986 | |
chr1 876482 12781001 SAMD11,NOC2L,KLHL17,PLEKHN1,C1orf170,HES4,ISG15,AGRN,AGRN,RP11-54O7.14,RP11-465B22.3,RP11-54O7.18,RP11-465B22.3,C1orf159,RP11-465B22.5,MIR429,TTLL10,TTLL10-AS1,TTLL10,TNFRSF18,TNFRSF4,SDF4,B3GALT6,FAM132A,UBE2J2,SCNN1D,ACAP3,ACAP3,PUSL1,PUSL1,CPSF3L,PUSL1,CPSF3L,GLTPD1,TAS1R3,DVL1,MXRA8,AURKAIP1,CCNL2,RP4-758J18.2,MRPL20,MRPL20,RN7SL657P,ANKRD65,ANKRD65,RP4-758J18.7,TMEM88B,VWA1,ATAD3C,ATAD3B,ATAD3A,TMEM240,SSU72,AL645728.2,SSU72,C1orf233,MIB2,RP11-345P4.9,MIB2,MMP23B,CDK11B,RP11-345P4.10,SLC35E2B,MMP23A,CDK11A,RP1-283E3.8,RP1-283E3.4,RP1-283E3.8,SLC35E2,SLC |
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[2017-10-26T09:46Z] System YAML configuration: /mnt/home_nfs1/mbeyens/local/share/bcbio/galaxy/bcbio_system.yaml | |
[2017-10-26T09:46Z] Resource requests: sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16 | |
[2017-10-26T09:46Z] Configuring 3 jobs to run, using 16 cores each with 32.1g of memory reserved for each job | |
[2017-10-26T09:46Z] Timing: organize samples | |
[2017-10-26T09:46Z] multiprocessing: organize_samples | |
[2017-10-26T09:46Z] Using input YAML configuration: /home/mbeyens/WGS_data/pair_analysis_1/config/run_paired_config.yaml | |
[2017-10-26T09:46Z] Checking sample YAML configuration: /home/mbeyens/WGS_data/pair_analysis_1/config/run_paired_config.yaml | |
[2017-10-26T09:46Z] Testing minimum versions of installed programs | |
[2017-10-26T09:47Z] Timing: alignment preparation | |
[2017-10-26T09:47Z] multiprocessing: prep_align_inputs |