@HD VN:1.5  SO:coordinate
@RG ID:LP6005441-DNA_C11    SM:LP6005441-DNA_C11
@PG ID:bwa  PN:bwa  VN:0.7.15-r1140 CL:/bix_tools/bwakit-0.7.15/bwa mem -p -t30 -H@RG\tID:LP6005441-DNA_C11\tSM:LP6005441-DNA_C11 -C /sbgenomics/Projects/92c61d0f-a072-4169-b5c7-767d29e937ba/f7e48782-bb07-4283-9537-0a8fa5b7584e/alt-aware-bwa-mem-workflow_Alt_aware_BWA_MEM/hs38DH.fa -
@PG ID:MarkDuplicates   VN:1.140(a81bc82e781dae05c922d1dbcee737334612399f_1444244284)   CL:picard.sam.markduplicates.MarkDuplicates INPUT=[/sbgenomics/Projects/92c61d0f-a072-4169-b5c7-767d29e937ba/f7e48782-bb07-4283-9537-0a8fa5b7584e/alt-aware-bwa-mem-workflow_Alt_aware_BWA_MEM/LP6005441-DNA_C11.hs38DH.aln.bam] OUTPUT=LP6005441-DNA_C11.hs38DH.aln.deduped.bam METRICS_FILE=LP6005441-DNA_C11.hs38DH.aln.metrics REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json  PN:MarkDuplicates
@SQ	SN:chr1	LN:248956422
HS2000-355_269:1:2307:11945:73421	147	chr1	10002	19	4S96M	=	10007	-91	CCCCAACCCCAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT	#####################################@;6;??;@55'HCFB=*FFD??*2GDGD?@HAHEGGHCHG@IIGGC<GBC;CAAFDBDBD@@?	XA:Z:chr1,-10106,7S39M1D32M1I21M,2;chr12,-10233,81M7D19M,10;chr20,+64287260,25M1I27M1D43M4S,4;chr18,-10001,24S21M1D55M,1;chr12_GL877875v1_alt,-233,81M7D19M,10;	MD:Z:5T37A52	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:2	AS:i:86	XS:i:78
HS2000-355_269:2:1108:12969:26408	99	chr1	10004	0	100M	=	10044	123	CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT	BCBFFFFFGGHHHJJJJIIJGIIIJIJIJIJII990?G=)?0?FH<GEF=CCFEE@G2=C?EE(;CB9;6@6(5??(559<?,9?AB239<2<8<928?8	MD:Z:100	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:0	AS:i:100	XS:i:100
HS2000-355_269:2:2312:2459:22449	99	chr1	10005	0	94M6S	=	10057	140	CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCTAACCGTAACTCTAACCCTAACCCTATCTCAA	@@@FFBFD8CDHHIBBHIIHIFHH3811)?:)?9):B)B#############################################################	MD:Z:56T16C4C15	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:3	AS:i:79	XS:i:79
HS2000-355_269:1:2307:11945:73421	99	chr1	10007	0	48M1D52M	=	10002	91	TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCATAACCCTAACCCTAACCCTAACCCTAACC	@@@DFFDEHFHFHHGIJJGIJGHIGEGGHIIFEEHEGHHBBAA;?B@F(B(;;=)==66=?EE>?@7;;A##############################	XA:Z:chr1,+10061,86M1D14M,2;chr12,+10044,48M1D52M,2;chr3,+10470,31M1I65M3S,2;chr4,-190122909,29M3D23M1D46M2S,4;chr18,+10029,66M1I33M,3;chr4,-190122830,52M1D11M1D37M,3;chr1,+10049,48M1D11M1I40M,3;chr1,-248946052,5M1D77M1D12M1D6M,4;chr20,-64287256,29M1I22M2D48M,4;chr1,+10126,21M1D79M,4;chr20,-64287310,52M3D30M1D18M,6;chr12_GL877875v1_alt,+44,48M1D52M,2;	MD:Z:48^T22C29	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:2	AS:i:88	XS:i:88	om:i:3
HS2000-355_269:1:1114:7529:75240	1123	chr1	10007	0	37M1D60M3S	=	10366	457	TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTCACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTACCC	@CCFFFFFDDAFB@GGHFGH@FHIFECBGAEC9CBBF?GFGDGIEGG>GCGI;=(8.6@=A)=???;?6;;66=2;;(,5<AB@5??#############	XA:Z:chr15,-101981029,100M,2;chr4,-190122948,100M,3;chrX,-156030570,62M1D38M,3;chr18,+10041,54M1I45M,3;chr4,+10078,100M,4;chr12,+10014,37M1D60M3S,3;chrX,-156030627,3S59M1D38M,3;chr18,-80262925,3S59M1D38M,3;chr3,+10392,65M1D35M,4;chr1,-248945958,14M1I85M,4;chr3,+10464,48M5D52M,7;chr3,+10605,80M1D10M1D10M,4;chr1,-248945908,10M1D13M1D77M,4;chr4,-190122897,46M3D16M1D38M,6;chr1,+180749,3S34M1D17M2D43M3S,4;chr1,-248946043,3S14M1D80M3S,4;chr4,+10001,2S54M2D44M,6;chr18,+10117,30M1D8M2D57M5S,5;chr19,-58607527,11S9M1D42M1D37M1S,3;chr3,+10000,4S33M1D23M1I23M16S,2;chr12_GL877875v1_alt,+14,37M1D60M3S,3;	MD:Z:37^A17A34T7	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:3	AS:i:80	XS:i:92
HS2000-355_269:2:2302:12695:6571	99	chr1	10012	0	40M1I56M3S	=	10056	128	CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCACA	@@@FBEFDDHHHHIIIIIFFAHGGHHGE??C8C;;FFB>;D>;@DEC@H(=FA@(==@)6=22)7;;?A>AA2;;;?@A#####################	MD:Z:96	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:1	AS:i:89	XS:i:89
HS2000-690_130:8:2104:17804:42012	99	chr1	10021	0	88M12S	=	10256	322	ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCCACCCCCACCC	CCCFFFFFHGDFHIIJJIIJJIGFHEHIIIJIGIEGDHHIIJJJHIHI=D(BC@FG2;=CEECH@CDF################################	XA:Z:chr22,-50808379,18S82M,0;chr4,-190122711,12S77M1I10M,1;chr12,+10232,85M15S,1;chr5,+11708,77M23S,0;chr18,-80262920,23S77M,0;chr21,-46699849,23M1D77M,5;chr13,-114354165,23S77M,0;chr18,+10131,16M1D12M1D72M,5;chr1,-248946173,82M4I6M2D8M,8;chr3,+10607,35M1I47M17S,2;chr3,+10136,1S30M1D6M1D18M1I33M11S,3;chr12_GL877875v1_alt,+232,85M15S,1;	MD:Z:76T5T5	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:2	AS:i:78	XS:i:82
HS2000-355_269:2:2213:5874:97462	99	chr1	10027	0	81M19S	=	10070	110	ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCAAACCCTAACCCTAACCACAACCCACACCCATATCT	@@@FDFADHDDBFG;CGB;BFHDHGGIG3CGGCC;9?GDF939BFG(B####################################################	XA:Z:chrX,-156030354,19S81M,2;chr12,+10232,76M24S,1;chr21,-46699875,19S81M,2;chr19,-58607537,21S79M,2;chr15,-101981059,19S29M1I51M,2;chr4,-190122978,19S29M1I51M,2;chr4,+10068,48M1I32M19S,2;chr1,-248945940,19S29M1I51M,2;chr1,-248946022,19S35M1D46M,3;chr3,+10458,4S44M1I15M1I16M19S,2;chr18,+10031,48M1I15M1I16M19S,3;chr3,+10518,53M1I27M19S,4;chr1,-248945689,37S63M,1;chr18,+10242,48M1I11M4D21M19S,6;chr3,-198173397,19S22M1I58M,4;chr18,+10462,48M1I11M4D21M19S,6;chr12_GL877875v1_alt,+232,76M24S,1;chr3_KI270784v1_alt,+62084,58M1I22M19S,4;	MD:Z:48A15T16	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:2	AS:i:71	XS:i:71
HS2000-355_269:2:1108:12969:26408	147	chr1	10044	0	18S76M1D6M	=	10004	-123	ACCCCCAACCCCACCCCAAACCCCAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCAACCCT	##########################A?9(95B=5','CC@?67HA=AAAHEGB=)GCFBB8GFD@B9IIHAD?GIG?G@IIGHEIHDAFFFFFDDF@@@	XA:Z:chr4,+190122818,6S76M18S,3;chr5,-10146,18S65M1D11M6S,3;chr5,-10206,18S65M1D11M6S,3;chr5,-10062,18S65M1D11M6S,3;chr5,-10134,18S65M1D11M6S,3;chr5,-10092,18S65M1D11M6S,3;chr5,-10074,18S65M1D11M6S,3;chr5,-10038,18S65M1D11M6S,3;chr5,-10044,18S65M1D11M6S,3;chr5,-10128,18S65M1D11M6S,3;chr5,-10014,18S65M1D11M6S,3;chr5,-10056,18S65M1D11M6S,3;chr5,-10116,18S65M1D11M6S,3;chr5,-10026,18S65M1D11M6S,3;chr5,-10176,18S65M1D11M6S,3;chr5,-10086,18S65M1D11M6S,3;chr5,-10104,18S65M1D11M6S,3;chr5,-10110,18S65M1D11M6S,3;chr5,-10080,18S65M1D11M6S,3;chr5,-10050,18S65M1D11M6S,3;chr5,-10230,18S65M1D11M6S,3;chr5,-10194,18S65M1D11M6S,3;chr5,-10152,18S65M1D11M6S,3;chr5,-10164,18S65M1D11M6S,3;chr5,-10002,18S65M1D11M6S,3;chr5,-10020,18S65M1D11M6S,3;chr5,-10158,18S65M1D11M6S,3;chr5,-10212,18S65M1D11M6S,3;chr5,-10224,18S65M1D11M6S,3;chr5,-10122,18S65M1D11M6S,3;chr5,-10182,18S65M1D11M6S,3;chr5,-10008,18S65M1D11M6S,3;chr5,-10188,18S65M1D11M6S,3;chr5,-10140,18S65M1D11M6S,3;chr5,-10170,18S65M1D11M6S,3;chr5,-10098,18S65M1D11M6S,3;chr5,-10032,18S65M1D11M6S,3;chr5,-10068,18S65M1D11M6S,3;chr5,-10218,18S65M1D11M6S,3;chr5,-10200,18S65M1D11M6S,3;chr3,-10590,26S68M1D6M,3;chr12,-10173,14S69M1D11M1D6M,5;chr10,+133787131,6S56M38S,0;chr11,-175728,28S66M6S,2;chr18,-9999,12S23M1D48M1D17M,6;chr12_GL877875v1_alt,-173,14S69M1D11M1D6M,5;	MD:Z:5T13A56^T6	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:3	AS:i:66	XS:i:61
HS2000-690_130:8:1215:11245:58923	163	chr1	10048	0	3S59M1I18M19S	=	10162	177	ACACTAACCCGAACCCTAACACAAACCCTAACCCTAACCCTAACCCTAACCCTAACGCGAACACCAACCATAACCCTAACCAACACACTAACGCTAACCC	=>;AAA+AAB6AA12?22?@*:)?1??ABB######################################################################	XA:Z:chr22,-50808004,19S78M3S,7;chr4,-190123032,44S51M5S,2;chr4,+10120,11S70M19S,6;chr12,-133265107,44S53M3S,3;chr12,-133264993,44S53M3S,3;chr12,-133264939,44S53M3S,3;chr12,-133264957,44S53M3S,3;chr12,-133265035,44S53M3S,3;chr12,-133265011,44S53M3S,3;chr12,-133265059,44S53M3S,3;chr12,-133265023,44S53M3S,3;chr12,+10061,3S53M44S,3;chr12,-133265119,44S53M3S,3;chr12,-133265089,44S53M3S,3;chr12,-133265065,44S53M3S,3;chr12,-133264987,44S53M3S,3;chr12,-133265029,44S53M3S,3;chr12,-133265131,44S53M3S,3;chr12,-133265125,44S53M3S,3;chr12,-133264981,44S53M3S,3;chr12,-133265071,44S53M3S,3;chr12,-133265137,44S53M3S,3;chr12,-133265101,44S53M3S,3;chr12,-133265005,44S53M3S,3;chr12,-133265083,44S53M3S,3;chr12,-133265077,44S53M3S,3;chr12,-133265095,44S53M3S,3;chr12,-133264975,44S53M3S,3;chr12,-133264945,44S53M3S,3;chr18,-80263049,44S53M3S,3;chr12,-133264999,44S53M3S,3;chr12,-133264969,44S53M3S,3;chr12,-133265041,44S53M3S,3;chr12,-133264963,44S53M3S,3;chrX,-156030475,44S53M3S,3;chr12,-133265047,44S53M3S,3;chr12,-133265113,44S53M3S,3;chr12,-133265017,44S53M3S,3;chr12,-133265053,44S53M3S,3;chr12,-133264951,44S53M3S,3;chr5,+11557,22M1D59M6I13M,16;chr15,-101981093,13M6I59M1D22M,16;chr7,-159335918,44S34M1D19M3S,3;chr20,-64287329,44S34M2D22M,5;chr9,-2824049,44S35M21S,0;chr17,+113252,22M2D34M44S,5;chr17,+113129,3S49M48S,3;chr1,+18254357,22S34M44S,0;chr10,-133787156,44S34M22S,0;chr1,+180918,22S34M44S,0;chr1,+10255,22S34M44S,0;chr17_GL383563v3_alt,+53252,22M2D34M44S,5;chr17_GL383563v3_alt,+53129,3S49M48S,3;	MD:Z:7T9C1T33C1T9C11	PG:Z:MarkDuplicates	RG:Z:LP6005441-DNA_C11	NM:i:7	AS:i:40	XS:i:43
