MBeyens

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

MBeyens

##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">

MBeyens

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

MBeyens

[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