Hi,
I must be doing something silly because all of my VCF files are empty (header, no results) after calling with Unified Genotyper. I'm using GATK version 2.7-2-g6bda569 with Java 1.7.00_40. The FASTQs were aligned with Novoalign.
java -Xmx4g -Djava.io.tmpdir=tmp -jar GenomeAnalysisTK.jar -R hg19_random.fa -D dbsnp_137.hg19.vcf -T UnifiedGenotyper -I data/gatk.realigned.recal.chr1-1-249250621.bam -o data/gatk.snps.raw.chr1-1-249250621.vcf -metrics data/gatk.snps.raw.chr1-1-249250621.vcf.metrics -L chr1:1-249250621 --computeSLOD -stand_call_conf 30 -stand_emit_conf 1 -nt 8 -K GATK_public.key -et NO_ET
Here is a snippet from my BAM file:
H801:144:C39TBACXX:7:2113:7016:95747 73 chr1 671881 20 101M = 671881 0 GCGGAGGCTGCCGTGACGTAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTCGGCCTGGAGAG YYYZZZZZZZZZZZZYZ]ZZ]]]YYYZ]]]ZZ]]]Z]Z]Z]]]]]Z]]]YZZZ]]]]ZYZZZZZZZZZYYYZZZZYYZZYZYZZZYZYZZZZZZZZZWXWW BD:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] MD:Z:101 PG:Z:novoalign RG:Z:SWID:testing:0 BI:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] NM:i:0 UQ:i:0 AS:i:0
H801:144:C39TBACXX:7:2302:11261:7162 153 chr1 971492 70 101M = 971492 0 GCTGTCTGTGAGGGCTGTGCTGAGGCCTTCCTGACCAGCACATGGGGTGGGAAGGACGACCTGGGGAATCCTGAAGTGATCTGAAGACAGAGCCCTGGGCT WYWXYZZZZZYZZXZYZZZYZZZZZZYYZZZZZZZZZZZZZZY]]]]ZZYYYZZZYYZZZZ]]]ZZZYZXZ]ZZZZZZYZ]]]]ZZYZZZZYZZZZZZYYY BD:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] MD:Z:101 PG:Z:novoalign RG:Z:SWID:testing:0 BI:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] NM:i:0 UQ:i:0 AS:i:0
H801:144:C39TBACXX:7:2302:13699:15898 153 chr1 971492 70 101M = 971492 0 GCTGTCTGTGAGGGCTGTGCTGAGGCCTTCCTGACCAGCACATGGGGTGGGAAGGACGACCTGGGGAATCCTGAAGTGATCTGAAGACAGAGCCCTGGGCT XYXZZYZZZZYZZZYYXYZZYZZZZZYYZZZZYYZZYYZZZYY]]]]]ZZZ]]]ZZZYZ]]Z]]Z]ZZZ]]]]]]ZZYZZ]]ZZYYYZYZXZZZZZZZYYX BD:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] MD:Z:101 PG:Z:novoalign RG:Z:SWID:testing:0 BI:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] NM:i:0 UQ:i:0 AS:i:0
H801:144:C39TBACXX:7:2206:12702:96307 97 chr1 987905 70 101M = 988021 217 GTGTGCATATGGGTCCATGTATGTGTGTGTATATGAGGGAGACACGCAGGTGTGTGTCTGAGTGTGTGCGCACATGGGTCCATGTATGTGTGTGTATAGGT YXYZZZZZZZZZZZZ]]]]ZZZ]ZZZYYZZZZ]]]]]]]Z]ZZ]Z]]]]ZZZZZZZYZZ]ZZXYYYWYYZWXWXYWWWYZZYZYZZZYZZZZWXWWYZZYW BD:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] MD:Z:101 PG:Z:novoalign RG:Z:SWID:testing:0 BI:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] NM:i:0 MQ:i:70 UQ:i:0 AS:i:0
H801:144:C39TBACXX:7:2206:12702:96307 145 chr1 988021 70 101M = 987905 -217 GTGTGTGTCCGTGTGTGTGCATGGGTCCATGTGTGTATAGTGTGTACACATGGGTCCATGTATGTGTGTGTATATGAGGGAGACACGCAGGTGTGTGTCCG WWWWWZXZXXWWWXZYWWWYWWWWWWWXWXZYXYWWYYWX]]]ZYXZZYZZ]]]]]]]Z]Z]]]]]]]]]]]]]Z]]]]]]]]]Z]]]ZZZZZZZZZZYYY BD:Z:]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]
And the output on the command line when running
INFO 12:44:55,654 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:44:55,656 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29
INFO 12:44:55,656 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 12:44:55,656 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 12:44:55,660 HelpFormatter - Program Args: -R hg19_random.fa -D dbsnp_137.hg19.vcf -T UnifiedGenotyper -I data/gatk.realigned.recal.chr1-1-249250621.bam -o data/gatk.snps.raw.chr1-1-249250621.vcf -metrics data/gatk.snps.raw.chr1-1-249250621.vcf.metrics -et NO_ET -L chr1:1-249250621 --computeSLOD -stand_call_conf 30 -stand_emit_conf 1 -nt 8 -K GATK_public.key
INFO 12:44:55,660 HelpFormatter - Date/Time: 2014/01/16 12:44:55
INFO 12:44:55,661 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:44:55,661 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:44:55,755 ArgumentTypeDescriptor - Dynamically determined type of dbsnp_137.hg19.vcf to be VCF
INFO 12:44:56,282 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:44:56,370 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 12:44:56,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:56,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
INFO 12:44:56,490 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:44:56,736 IntervalUtils - Processing 249250621 bp from intervals
INFO 12:44:56,749 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 1 CPU thread(s) for each of 8 data thread(s), of 24 processors available on this machine
INFO 12:44:56,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 12:44:56,992 GenomeAnalysisEngine - Done preparing for traversal
INFO 12:44:56,992 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 12:44:56,992 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 12:44:57,085 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:57,090 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00
INFO 12:44:57,095 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:57,101 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 12:44:57,105 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:57,108 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:44:57,112 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 12:44:57,114 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:57,124 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 12:44:57,129 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:57,140 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 12:44:57,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:57,177 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 12:44:57,186 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 12:44:57,191 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.00
INFO 12:44:57,285 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:44:57,482 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:44:57,655 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:44:57,827 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:44:57,996 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:44:58,301 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_137.hg19.vcf
INFO 12:45:26,995 ProgressMeter - chr1:93237277 9.18e+07 30.0 s 0.0 s 37.4% 80.0 s 50.0 s
INFO 12:45:56,999 ProgressMeter - chr1:200739385 1.99e+08 60.0 s 0.0 s 80.5% 74.0 s 14.0 s
INFO 12:46:12,672 ProgressMeter - done 2.49e+08 75.0 s 0.0 s 100.0% 75.0 s 0.0 s
INFO 12:46:12,673 ProgressMeter - Total runtime 75.68 secs, 1.26 min, 0.02 hours
INFO 12:46:12,673 MicroScheduler - 5225 reads were filtered out during the traversal out of approximately 500463 total reads (1.04%)
INFO 12:46:12,673 MicroScheduler - -> 5225 reads (1.04% of total) failing BadMateFilter
INFO 12:46:12,673 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 12:46:12,673 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 12:46:12,674 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 12:46:12,674 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 12:46:12,674 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 12:46:12,674 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
Can anyone tell me what might be wrong? It's reliably failing for every chromosome on reasonably-sized data (this BAM is 20M with ~500k reads).
Thanks in advance
