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Created 2014-06-03 11:58:36 | Updated 2014-06-03 12:10:00 | Tags: baserecalibrator vcf vcftools index-file
Comments (9)

I am performing analysis on mm9 (mouse). Downloaded VCF file from UCSC. Removed chr*_random and chrM Used vcftool v4.0 prepared two files ONLY INDEL and ONLY SNPS vcf files (DBINDEL, DBSNP) Please kindly suggest me what needs to be done in this case? Command used java -Xmx30g -XX:+UseGCOverheadLimit -jar GenomeAnalysisTK.3.1-1-g07a4bf8.jar --log_to_file gatk.realigned.fixed.log --performanceLog gatk.realigned.fixed.perflog --keep_program_records -T BaseRecalibrator -R REFERENCE -I INPUTBAMNAME.realigned.fixed.bam -o OUTPUT_table --knownSites DBINDEL --knownSites DBSNP --deletions_default_quality 45 --insertions_default_quality 45 --low_quality_tail 2 --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED --solid_recal_mode SET_Q_ZERO --lowMemoryMode --no_standard_covs --bqsrBAQGapOpenPenalty 30.0

some times I get this error: NFO 12:42:13,747 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-g07a4bf8, Compiled 2014/03/18 06:09:21 INFO 12:42:13,748 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 12:42:13,748 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 12:42:13,752 HelpFormatter - Program Args: --log_to_file /media/NAS1/PFlab/Mano/AllBAM/GATK/QualityScore/H3K4me1_run22_F3_5.sorted.marked.gatk.realigned.fixed.log --performanceLog /media/NAS1/PFlab/Mano/AllBAM/GATK/QualityScore/H3K4me1_run22_F3_5.sorted.marked.gatk.realigned.fixed.perflog --keep_program_records -T BaseRecalibrator -R /media/NAS1/PFlab/Mano/Genome/reference.fa -I /media/NAS1/PFlab/Mano/AllBAM/GATK/H3K4me1_run22_F3_5.sorted.marked.intervals.realigned.fixed.bam -o /media/NAS1/PFlab/Mano/AllBAM/GATK/QualityScore/H3K4me1_run22_F3_5.sorted.marked.intervals.realigned.after_recal_data.table --knownSites /media/NAS1/PFlab/Mano/Fwithoutchrsorted.vcf --knownSites /media/NAS1/PFlab/Mano/New.SNPs_only_withoutCHR_sort.vcf --deletions_default_quality 45 --insertions_default_quality 45 --low_quality_tail 2 --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED --solid_recal_mode SET_Q_ZERO --lowMemoryMode --no_standard_covs --bqsrBAQGapOpenPenalty 30.0 INFO 12:42:13,756 HelpFormatter - Executing as mano@balrog01 on Linux 3.2.0-27-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13. INFO 12:42:13,756 HelpFormatter - Date/Time: 2014/06/03 12:42:13 INFO 12:42:13,756 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:42:13,757 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:42:14,556 GenomeAnalysisEngine - Strictness is SILENT INFO 12:42:14,634 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 12:42:14,643 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 12:42:14,687 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04 INFO 12:42:15,979 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:171) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadFromDisk(RMDTrackBuilder.java:324) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(RMDTrackBuilder.java:308) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(RMDTrackBuilder.java:267) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(RMDTrackBuilder.java:213) at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(RMDTrackBuilder.java:140) at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool. (ReferenceOrderedDataSource.java:208) at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource. (ReferenceOrderedDataSource.java:88) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(GenomeAnalysisEngine.java:973) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:767) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:284) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:526) at org.broad.tribble.index.IndexFactory.loadIndex(IndexFactory.java:167) ... 14 more Caused by: java.io.EOFException at org.broad.tribble.util.LittleEndianInputStream.readFully(LittleEndianInputStream.java:134) at org.broad.tribble.util.LittleEndianInputStream.readLong(LittleEndianInputStream.java:76) at org.broad.tribble.index.linear.LinearIndex$ChrIndex.read(LinearIndex.java:268) at org.broad.tribble.index.AbstractIndex.read(AbstractIndex.java:359) at org.broad.tribble.index.linear.LinearIndex. (LinearIndex.java:98) ... 19 more
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
ERROR ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem. ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR ##### ERROR MESSAGE: java.lang.reflect.InvocationTargetException
ERROR ------------------------------------------------------------------------------------------

Current error: INFO 13:49:09,583 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-g07a4bf8, Compiled 2014/03/18 06:09:21 INFO 13:49:09,583 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:49:09,583 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 13:49:09,588 HelpFormatter - Program Args: --log_to_file /home/mano/media/NAS1/PFlab/Mano/AllBAM/GATK/QualityScore/H3K4me1_run22_F3_5.sorted.marked.gatk.realigned.fixed.log --performanceLog /home/mano/media/NAS1/PFlab/Mano/AllBAM/GATK/QualityScore/H3K4me1_run22_F3_5.sorted.marked.gatk.realigned.fixed.perflog --keep_program_records -T BaseRecalibrator -R /home/mano/media/NAS1/PFlab/Mano/Genome/reference.fa -I /home/mano/media/NAS1/PFlab/Mano/AllBAM/GATK/H3K4me1_run22_F3_5.sorted.marked.intervals.realigned.fixed.bam -o /home/mano/media/NAS1/PFlab/Mano/AllBAM/GATK/QualityScore/H3K4me1_run22_F3_5.sorted.marked.intervals.realigned.after_recal_data.table --knownSites /home/mano/media/NAS1/PFlab/Mano/Fwithoutchrsorted.vcf --knownSites /home/mano/media/NAS1/PFlab/Mano/SNPs_only_withoutCHR_sort.vcf --deletions_default_quality 45 --insertions_default_quality 45 --low_quality_tail 2 --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED --solid_recal_mode SET_Q_ZERO --lowMemoryMode --no_standard_covs --bqsrBAQGapOpenPenalty 30.0 INFO 13:49:09,591 HelpFormatter - Executing as mano@balrog04 on Linux 3.2.0-26-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13. INFO 13:49:09,592 HelpFormatter - Date/Time: 2014/06/02 13:49:09 INFO 13:49:09,592 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:49:09,592 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:49:10,461 GenomeAnalysisEngine - Strictness is SILENT INFO 13:49:10,538 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 13:49:10,547 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 13:49:10,574 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 INFO 13:50:17,644 RMDTrackBuilder - Writing Tribble index to disk for file /home/mano/media/NAS1/PFlab/Mano/SNPs_only_withoutCHR_sort.vcf.idx INFO 13:50:29,885 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8):
ERROR ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR ##### ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR ##### ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR ##### ERROR MESSAGE: I/O error loading or writing tribble index file for /home/mano/media/NAS1/PFlab/Mano/SNPs_only_withoutCHR_sort.vcf
ERROR ------------------------------------------------------------------------------------------

Please note that .idx file is formed but only in Kilobytes


Created 2013-11-14 16:35:47 | Updated | Tags: selectvariants variantfiltration vcf plink vcftools
Comments (1)

Hi,

I was wondering if you could use the toolkit to generate a separate VCF file containing only SNPs that are found at a predetermined chromosome and base pair position. I have a plink file which I want to convert back to VCF format and it seems unbelievably hard to do so I thought this may be a good way to get around that problem?

I am aware that vcftools offers this function with the "--positions " option, however for some reason I am getting far more variants than I listed and there is nothing wrong that is obvious with my listed positions/vcf file.

Thanks in advance, Danica