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February 20, 2018 23:14
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| ##fileformat=VCFv4.2 | |
| ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | |
| ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> | |
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> | |
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> | |
| ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> | |
| ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> | |
| ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="The phred-scaled genotype likelihoods rounded to the closest integer"> | |
| ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias"> | |
| ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | |
| ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> | |
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Combined depth across samples"> | |
| ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> | |
| ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> | |
| ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> | |
| ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele, in the same order as listed"> | |
| ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele, in the same order as listed"> | |
| ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | |
| ##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS mapping quality"> | |
| ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | |
| ##SentieonCommandLine.Haplotyper=<ID=Haplotyper,Version="sentieon-genomics-201704.03",Date="2017-12-22T16:56:50Z",CommandLine="/scratch/ucgd/lustre/ugpuser/apps/kingspeak.peaks/sentieon/201704.03/libexec/driver --reference /scratch/ucgd/lustre/ugpuser/ucgd_data/references/human_g1k_v37_decoy.fasta --input 14363X13.bam --interval /scratch/local/ugp_hjHgyJ/intervals_kv40C.bed --thread_count 20 --qual_cal /scratch/local/ugp_hjHgyJ/0.recal.table --algo Haplotyper --emit_conf 30 --min_base_qual 20 --call_conf 30 --emit_mode gvcf /scratch/local/ugp_hjHgyJ/0.g.vcf.gz"> | |
| ##contig=<ID=1,length=249250621,assembly=b37> | |
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| ##contig=<ID=X,length=155270560,assembly=b37> | |
| ##contig=<ID=Y,length=59373566,assembly=b37> | |
| ##contig=<ID=MT,length=16569,assembly=b37> | |
| ##contig=<ID=GL000207.1,length=4262,assembly=b37> | |
| ##contig=<ID=GL000226.1,length=15008,assembly=b37> | |
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| ##contig=<ID=GL000210.1,length=27682,assembly=b37> | |
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| ##contig=<ID=GL000247.1,length=36422,assembly=b37> | |
| ##contig=<ID=GL000245.1,length=36651,assembly=b37> | |
| ##contig=<ID=GL000197.1,length=37175,assembly=b37> | |
| ##contig=<ID=GL000203.1,length=37498,assembly=b37> | |
| ##contig=<ID=GL000246.1,length=38154,assembly=b37> | |
| ##contig=<ID=GL000249.1,length=38502,assembly=b37> | |
| ##contig=<ID=GL000196.1,length=38914,assembly=b37> | |
| ##contig=<ID=GL000248.1,length=39786,assembly=b37> | |
| ##contig=<ID=GL000244.1,length=39929,assembly=b37> | |
| ##contig=<ID=GL000238.1,length=39939,assembly=b37> | |
| ##contig=<ID=GL000202.1,length=40103,assembly=b37> | |
| ##contig=<ID=GL000234.1,length=40531,assembly=b37> | |
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| ##contig=<ID=GL000191.1,length=106433,assembly=b37> | |
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| ##contig=<ID=GL000228.1,length=129120,assembly=b37> | |
| ##contig=<ID=GL000214.1,length=137718,assembly=b37> | |
| ##contig=<ID=GL000221.1,length=155397,assembly=b37> | |
| ##contig=<ID=GL000209.1,length=159169,assembly=b37> | |
| ##contig=<ID=GL000218.1,length=161147,assembly=b37> | |
| ##contig=<ID=GL000220.1,length=161802,assembly=b37> | |
| ##contig=<ID=GL000213.1,length=164239,assembly=b37> | |
| ##contig=<ID=GL000211.1,length=166566,assembly=b37> | |
| ##contig=<ID=GL000199.1,length=169874,assembly=b37> | |
| ##contig=<ID=GL000217.1,length=172149,assembly=b37> | |
| ##contig=<ID=GL000216.1,length=172294,assembly=b37> | |
| ##contig=<ID=GL000215.1,length=172545,assembly=b37> | |
| ##contig=<ID=GL000205.1,length=174588,assembly=b37> | |
| ##contig=<ID=GL000219.1,length=179198,assembly=b37> | |
| ##contig=<ID=GL000224.1,length=179693,assembly=b37> | |
| ##contig=<ID=GL000223.1,length=180455,assembly=b37> | |
| ##contig=<ID=GL000195.1,length=182896,assembly=b37> | |
| ##contig=<ID=GL000212.1,length=186858,assembly=b37> | |
| ##contig=<ID=GL000222.1,length=186861,assembly=b37> | |
| ##contig=<ID=GL000200.1,length=187035,assembly=b37> | |
| ##contig=<ID=GL000193.1,length=189789,assembly=b37> | |
| ##contig=<ID=GL000194.1,length=191469,assembly=b37> | |
| ##contig=<ID=GL000225.1,length=211173,assembly=b37> | |
| ##contig=<ID=GL000192.1,length=547496,assembly=b37> | |
| ##contig=<ID=NC_007605,length=171823,assembly=b37> | |
| ##contig=<ID=hs37d5,length=35477943,assembly=b37> | |
| ##contig=<ID=phix,length=5386,assembly=b37> | |
| ##reference=file:///scratch/ucgd/lustre/ugpuser/ucgd_data/references/human_g1k_v37_decoy.fasta | |
| ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) | |
| ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) | |
| ##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) | |
| ##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) | |
| ##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) | |
| ##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) | |
| ##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) | |
| ##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) | |
| ##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) | |
| ##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) | |
| ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) | |
| ##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) | |
| ##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) | |
| ##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) | |
| ##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) | |
| ##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) | |
| ##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) | |
| ##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) | |
| ##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) | |
| ##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) | |
| ##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) | |
| ##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) | |
| ##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) | |
| ##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) | |
| ##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) | |
| ##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) | |
| ##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) | |
| ##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) | |
| ##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) | |
| ##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) | |
| ##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) | |
| ##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) | |
| ##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) | |
| ##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) | |
| ##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) | |
| ##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) | |
| ##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) | |
| ##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) | |
| ##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) | |
| ##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) | |
| ##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) | |
| ##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) | |
| ##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) | |
| ##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) | |
| ##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) | |
| ##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) | |
| ##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) | |
| ##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) | |
| ##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) | |
| ##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) | |
| ##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) | |
| ##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) | |
| ##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) | |
| ##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) | |
| ##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) | |
| ##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) | |
| ##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) | |
| ##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) | |
| ##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) | |
| ##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) | |
| ##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) | |
| ##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) | |
| ##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) | |
| ##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) | |
| ##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive) |
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