Question: GATK GenotypeGVCFs output is empty gvcf file
0
gravatar for GK1610
12 months ago by
GK161060
United States
GK161060 wrote:

I ran

 java -Xmx48g -jar gatk/3.5-0/src/GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19/hg19.fa -V merged.240samples.chr22.gvcf.gz -o merged.jointGT.chr22.gvcf.gz

it got successfully completed

INFO  20:18:40,706 ProgressMeter - Total runtime 9474.26 secs, 157.90 min, 2.63 hours
[
INFO  17:40:45,466 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:40:45,469 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO  17:40:45,469 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  17:40:45,469 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  17:40:45,472 HelpFormatter - Program Args: -T GenotypeGVCFs -R hg19/hg19.fa -V merged.240samples.chr22.gvcf.gz -o merged.jointGT.chr22.gvcf.gz
INFO  17:40:45,476 HelpFormatter - Executing as blahblah@node23-17 on Linux  amd64; Java HotSpot(TM) 64-Bit 
INFO  17:40:45,476 HelpFormatter - Date/Time: 2018/03/28 17:40:45
INFO  17:40:45,476 HelpFormatter - ----------------------------------


unfortunately my outputfile is empty
this is my empty output gvcf file

##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any="" possible="" alternative="" allele="" at="" this="" location"="">
##FILTER=<ID=LowQual,Description="Low quality"="">
##FILTER=<ID=PASS,Description="All filters="" passed"="">
##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="Approximate read="" depth="" (reads="" with="" MQ="255" or="" with="" bad="" mates="" are="" filtered)"="">
##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="Normalized, Phred-scaled="" likelihoods="" for="" genotypes="" as="" defined="" in="" the="" VCF="" specification"="">
##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference="" genotype="" confidence,="" encoded="" as="" a="" phred="" quality="" -10*log10="" p(genotype="" call="" is="" wrong)"="">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component="" statistics="" which="" comprise="" the="" Fisher's="" Exact="" Test="" to="" detect="" strand="" bias."="">
##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.5-0-g36282e4,Date="Wed Mar="" 28="" 17:40:46="" EDT="" 2018",Epoch="1522273246553,CommandLineOptions="analysis_type=GenotypeGVCFs" input_file="[]" show="" ##GATKCommandLine.HaplotypeCaller="&lt;ID=HaplotypeCaller,Version=3.5-0-g36282e4,Date="Fri" Dec="" 09="" 08:21:43="" EST="" 2016",Epoch="1481289703015,CommandLineOptions="analysis_type=HaplotypeCaller" input_file="[" ##GATKCommandLine.SelectVariants="&lt;ID=SelectVariants,Version=3.5-0-g36282e4,Date="Wed" Mar="" 21="" 22:41:46="" EDT="" 2018",Epoch="1521686506383,CommandLineOptions="analysis_type=SelectVariants" input_file="[]" s="" ##GATKCommandLine="&lt;ID=CombineGVCFs,CommandLine="CombineGVCFs" --output="" merged..chr22.gvcf.gz="" --variant="" scratch="" meta-mer="" ##GVCFBlock0-1="minGQ=0(inclusive),maxGQ=1(exclusive)" ##GVCFBlock1-2="minGQ=1(inclusive),maxGQ=2(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)" ##GVCFBlock2-3="minGQ=2(inclusive),maxGQ=3(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)" ##GVCFBlock3-4="minGQ=3(inclusive),maxGQ=4(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)" ##GVCFBlock4-5="minGQ=4(inclusive),maxGQ=5(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)" ##GVCFBlock5-6="minGQ=5(inclusive),maxGQ=6(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)" ##GVCFBlock6-7="minGQ=6(inclusive),maxGQ=7(exclusive)" ##GVCFBlock60-70="minGQ=60(inclusive),maxGQ=70(exclusive)" ##GVCFBlock7-8="minGQ=7(inclusive),maxGQ=8(exclusive)" ##GVCFBlock70-80="minGQ=70(inclusive),maxGQ=80(exclusive)" ##GVCFBlock8-9="minGQ=8(inclusive),maxGQ=9(exclusive)" ##GVCFBlock80-90="minGQ=80(inclusive),maxGQ=90(exclusive)" ##GVCFBlock9-10="minGQ=9(inclusive),maxGQ=10(exclusive)" ##GVCFBlock90-99="minGQ=90(inclusive),maxGQ=99(exclusive)" ##GVCFBlock99-2147483647="minGQ=99(inclusive),maxGQ=2147483647(exclusive)" ##INFO="&lt;ID=AC,Number=A,Type=Integer,Description="Allele" count="" in="" genotypes,="" for="" each="" ALT="" allele,="" in="" the="" same="" order="" as="" listed"="">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency,="" for="" each="" ALT="" allele,="" in="" the="" same="" order="" as="" listed"="">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number="" of="" alleles="" in="" called="" genotypes"="">
##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="Approximate read="" depth;="" some="" reads="" may="" have="" been="" filtered"="">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any="" of="" the="" samples="" downsampled?"="">
##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=FS,Number=1,Type=Float,Description="Phred-scaled p-value="" using="" Fisher's="" exact="" test="" to="" detect="" strand="" bias"="">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of="" the="" site="" with="" at="" most="" two="" segregating="" haplotypes"="">
##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="" (not="" necessarily="" the="" same="" as="" the="" AC),="" for="" each="" ALT="" allele,="" in="" the="" same="" order="" as="" list="" ##INFO="&lt;ID=MLEAF,Number=A,Type=Float,Description="Maximum" likelihood="" expectation="" (MLE)="" for="" the="" allele="" frequency="" (not="" necessarily="" the="" same="" as="" the="" AF),="" for="" each="" ALT="" allele,="" in="" the="" same="" order="" as="" lis="" ##INFO="&lt;ID=MQ,Number=1,Type=Float,Description="RMS" Mapping="" Quality"="">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From="" Wilcoxon="" rank="" sum="" test="" of="" Alt="" vs.="" Ref="" read="" mapping="" qualities"="">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence="" Quality="" by="" Depth"="">
##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"="">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds="" Ratio="" of="" 2x2="" contingency="" table="" to="" detect="" strand="" bias"="">
##bcftools_viewCommand=view -m2 -M2 meta-merged.1.chr22.gvcf.gz; Date=Tue Mar 27 12:42:50 2018
##bcftools_viewVersion=1.7+htslib-1.7
##contig=<ID=chr1,length=249250621,assembly=hg19>
##contig=<ID=chr10,length=135534747,assembly=hg19>
##contig=<ID=chr11,length=135006516,assembly=hg19>
##contig=<ID=chr12,length=133851895,assembly=hg19>
##contig=<ID=chr13,length=115169878,assembly=hg19>
##contig=<ID=chr14,length=107349540,assembly=hg19>
##contig=<ID=chr15,length=102531392,assembly=hg19>
##contig=<ID=chr16,length=90354753,assembly=hg19>
##contig=<ID=chr17,length=81195210,assembly=hg19>
##contig=<ID=chr18,length=78077248,assembly=hg19>
##contig=<ID=chr19,length=59128983,assembly=hg19>
##contig=<ID=chr2,length=243199373,assembly=hg19>
##contig=<ID=chr20,length=63025520,assembly=hg19>
##contig=<ID=chr21,length=48129895,assembly=hg19>
##contig=<ID=chr22,length=51304566,assembly=hg19>
##contig=<ID=chr3,length=198022430,assembly=hg19>
##contig=<ID=chr4,length=191154276,assembly=hg19>
##contig=<ID=chr5,length=180915260,assembly=hg19>
##contig=<ID=chr6,length=171115067,assembly=hg19>
##contig=<ID=chr7,length=159138663,assembly=hg19>
##contig=<ID=chr8,length=146364022,assembly=hg19>
##contig=<ID=chr9,length=141213431,assembly=hg19>
##contig=<ID=chrM,length=16571,assembly=hg19>
##contig=<ID=chrX,length=155270560,assembly=hg19>
##contig=<ID=chrY,length=59373566,assembly=hg19>
##reference=/resources/hg19/hg19.fa
##source=CombineGVCFs
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample_PFC_1130_A sample_PFC_1131_A sample_PFC_1132_A sample_PFC_1135_A sample_PFC_1136_A........



My input file

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  MSSM_PFC_1130_A MSSM_PFC_1131_A sample_PFC_1132_A sample_PFC_1135_A sample PFC_1136_A sample_PFC_1138_A sample_PFC_1139_A sample_PFC_11
chr22   1       .       N       <NON_REF>       .       .       END=16050000    GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050001        .       G       <NON_REF>       .       .       END=16050002    GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.
chr22   16050003        .       T       <NON_REF>       .       .       END=16050007    GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.
chr22   16050008        .       T       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050009        .       A       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050010        .       A       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050011        .       G       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050012        .       T       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050013        .       C       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050014        .       C       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050015        .       C       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22   16050016        .       A       <NON_REF>       .       .       .       GT:DP:GQ:MIN_DP:PL      ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
snp • 644 views
ADD COMMENTlink modified 12 months ago by Pierre Lindenbaum119k • written 12 months ago by GK161060
0
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:
My input file

(...)

all your lines are <NON_REF> in the g.vcf file. These are 'blocks' of coverage statistically equivalent. But there is no variant here.

ADD COMMENTlink written 12 months ago by Pierre Lindenbaum119k
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