HaplotypeCaller/UnifiedGenotyper produce no output
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Hi, I'm using version 2.5-2 of GATK and until recently I was using version 2.3 of the Bundle.

a few weeks ago I ran UnifiedGenotyper on WGS data (converted to Bam from Complete Genomics and processed with GATK) and got my list of variants using hg19 downloaded from UCSC [with chrM at the end] and having modified the bundle dbsnp vcfs to match. However I needed to go back earlier this week and re-run it so I decided to use the v2.5 of the Bundle and HaplotypeCaller. When I didn't get any output (see below) I tried again with the UnifiedGenotyper. The command I used for the UnifiedGenotyper is:

java -Xmx24g -Xms24g -jar ~/apps/gatk/GenomeAnalysisTK.jar -I 14972_realigned.bam -I 14973_realigned.bam -R ~/gatk/ucsc.hg19.fasta -T UnifiedGenotyper -o twins.UG.vcf -nt 12 -stand_emit_conf 10.0 -stand_call_conf 30.0 --dbsnp ~/gatk/dbsnp_137.hg19.vcf -glm BOTH -dcov 200 > twins_UG.log 2>&1

using either HaplotypeCaller or UnifiedGenotyper with either the ucsc.hg19.fasta or hg19 [with chrM at the beginning, modified to match the vcfs] I was unable to get any output. Let me clarify that - the output VCF files was produced containing the full header but no variants and the log file looks like this:

INFO 06:34:41,404 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:34:41,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02 INFO 06:34:41,411 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 06:34:41,411 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 06:34:41,414 HelpFormatter - Program Args: -I 14972_realigned.bam -I 14973_realigned.bam -R /Users/thompsoni/gatk/ucsc.hg19.fasta -T UnifiedGenotyper -o twins.UG.vcf -nt 12 -stand_emit_conf 10.0 -stand_call_conf 30.0 --dbsnp /Users/thompsoni/gatk/dbsnp_137.hg19.vcf -glm BOTH -dcov 200 INFO 06:34:41,415 HelpFormatter - Date/Time: 2013/05/20 06:34:41 INFO 06:34:41,415 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:34:41,415 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:34:41,448 ArgumentTypeDescriptor - Dynamically determined type of /Users/thompsoni/gatk/dbsnp_137.hg19.vcf to be VCF INFO 06:34:41,580 GenomeAnalysisEngine - Strictness is SILENT INFO 06:34:41,660 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 200 INFO 06:34:41,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:34:41,688 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 06:34:41,699 RMDTrackBuilder - Creating Tribble index in memory for file /Users/thompsoni/gatk/dbsnp_137.hg19.vcf INFO 06:38:01,508 RMDTrackBuilder - Writing Tribble index to disk for file /Users/thompsoni/gatk/dbsnp_137.hg19.vcf.idx INFO 06:38:20,936 MicroScheduler - Running the GATK in parallel mode with 12 total threads, 1 CPU thread(s) for each of 12 data thread(s), of 24 processors available on this machine INFO 06:38:21,082 GenomeAnalysisEngine - Creating shard strategy for 2 BAM files INFO 06:38:21,708 GenomeAnalysisEngine - Done creating shard strategy INFO 06:38:21,708 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 06:38:21,708 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 06:38:21,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,843 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,877 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 INFO 06:38:21,878 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,908 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 06:38:21,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,923 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,924 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,939 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,940 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 06:38:21,976 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,092 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12 INFO 06:38:22,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,242 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12 INFO 06:38:22,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17 INFO 06:38:22,611 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09 INFO 06:38:51,715 ProgressMeter - Starting 0.00e+00 30.0 s 49.6 w 100.0% 30.0 s 0.0 s INFO 06:39:21,719 ProgressMeter - Starting 0.00e+00 60.0 s 99.2 w 100.0% 60.0 s 0.0 s INFO 06:39:51,724 ProgressMeter - Starting 0.00e+00 90.0 s 148.8 w 100.0% 90.0 s 0.0 s INFO 06:40:21,728 ProgressMeter - Starting 0.00e+00 120.0 s 198.4 w 100.0% 120.0 s 0.0 s INFO 06:40:51,732 ProgressMeter - Starting 0.00e+00 2.5 m 248.1 w 100.0% 2.5 m 0.0 s INFO 06:41:21,735 ProgressMeter - Starting 0.00e+00 3.0 m 297.7 w 100.0% 3.0 m 0.0 s INFO 06:41:51,739 ProgressMeter - Starting 0.00e+00 3.5 m 347.3 w 100.0% 3.5 m 0.0 s INFO 06:42:21,743 ProgressMeter - Starting 0.00e+00 4.0 m 396.9 w 100.0% 4.0 m 0.0 s INFO 06:42:51,748 ProgressMeter - Starting 0.00e+00 4.5 m 446.5 w 100.0% 4.5 m 0.0 s INFO 06:43:21,751 ProgressMeter - Starting 0.00e+00 5.0 m 496.1 w 100.0% 5.0 m 0.0 s INFO 06:43:51,755 ProgressMeter - Starting 0.00e+00 5.5 m 545.7 w 100.0% 5.5 m 0.0 s INFO 06:44:21,759 ProgressMeter - Starting 0.00e+00 6.0 m 595.3 w 100.0% 6.0 m 0.0 s INFO 06:44:51,763 ProgressMeter - 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Whilst I have managed to rerun UnifiedGenotyper with my unmodified hg19 [chrM at the end] and modified dbsnp vcf, I am curious as to why this should be a problem as I would prefer to use the vcfs and references without modifications.


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