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Created 2013-12-03 17:47:15 | Updated 2013-12-03 18:03:12 | Tags: realignertargetcreator filters
Comments (9)

Dear all can anybody help me with this error while running Realigntargetcreator the run failed to pass through many filters any suggestion why

Run summary

INFO 12:07:39,628 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 12:07:39,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29 
INFO 12:07:39,631 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO 12:07:39,631 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO 12:07:39,635 HelpFormatter - Program Args: -T RealignerTargetCreator -R /home/sab/ref/human_hg19.fa -I /home/sab/pipeline/A_sorted.bam -o /home/sab/pipeline/A_sorted.IndelRealigner.intervals 
INFO 12:07:39,636 HelpFormatter - Date/Time: 2013/12/03 12:07:39 
INFO 12:07:39,636 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 12:07:39,636 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 12:07:39,697 GenomeAnalysisEngine - Strictness is SILENT 
INFO 12:07:39,789 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO 12:07:39,798 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO 12:07:39,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO 12:07:39,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO 12:07:40,400 GenomeAnalysisEngine - Done preparing for traversal 
INFO 12:07:40,400 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO 12:07:40,401 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining 
INFO 12:08:10,406 ProgressMeter - chr1:85262337 8.53e+07 30.0 s 0.0 s 2.8% 18.2 m 17.7 m 
INFO 12:08:40,407 ProgressMeter - chr1:180404225 1.80e+08 60.0 s 0.0 s 5.8% 17.2 m 16.2 m 
INFO 12:09:10,409 ProgressMeter - chr2:26489345 2.76e+08 90.0 s 0.0 s 8.9% 16.8 m 15.3 m 
INFO 12:09:40,413 ProgressMeter - chr2:126159101 3.75e+08 120.0 s 0.0 s 12.1% 16.5 m 14.5 m 
INFO 12:10:10,415 ProgressMeter - chr2:226503317 4.76e+08 2.5 m 0.0 s 15.4% 16.3 m 13.8 m 
INFO 12:10:40,417 ProgressMeter - chr3:79985305 5.72e+08 3.0 m 0.0 s 18.5% 16.2 m 13.2 m 
INFO 12:11:10,418 ProgressMeter - chr3:178616501 6.71e+08 3.5 m 0.0 s 21.7% 16.1 m 12.6 m 
INFO 12:11:40,424 ProgressMeter - chr4:82438805 7.73e+08 4.0 m 0.0 s 25.0% 16.0 m 12.0 m 
INFO 12:12:10,426 ProgressMeter - chr4:190799281 8.81e+08 4.5 m 0.0 s 28.5% 15.8 m 11.3 m 
INFO 12:12:40,427 ProgressMeter - chr5:95948005 9.78e+08 5.0 m 0.0 s 31.6% 15.8 m 10.8 m 
INFO 12:13:10,429 ProgressMeter - chr6:6479181 1.07e+09 5.5 m 0.0 s 34.5% 15.9 m 10.4 m 
INFO 12:13:40,430 ProgressMeter - chr6:92259205 1.15e+09 6.0 m 0.0 s 37.3% 16.1 m 10.1 m 
INFO 12:14:10,432 ProgressMeter - chr7:12978229 1.25e+09 6.5 m 0.0 s 40.3% 16.1 m 9.6 m 
INFO 12:14:40,433 ProgressMeter - chr7:102060237 1.34e+09 7.0 m 0.0 s 43.1% 16.2 m 9.2 m 
INFO 12:15:10,435 ProgressMeter - chr8:37320269 1.43e+09 7.5 m 0.0 s 46.2% 16.2 m 8.7 m 
INFO 12:15:40,436 ProgressMeter - chr8:134665297 1.53e+09 8.0 m 0.0 s 49.3% 16.2 m 8.2 m 
INFO 12:16:10,437 ProgressMeter - chr9:94340989 1.63e+09 8.5 m 0.0 s 52.8% 16.1 m 7.6 m 
INFO 12:16:40,439 ProgressMeter - chr10:51925797 1.73e+09 9.0 m 0.0 s 56.0% 16.1 m 7.1 m 
INFO 12:17:10,440 ProgressMeter - chr11:10504845 1.83e+09 9.5 m 0.0 s 59.0% 16.1 m 6.6 m 
INFO 12:17:40,442 ProgressMeter - chr11:102575141 1.92e+09 10.0 m 0.0 s 62.0% 16.1 m 6.1 m 
INFO 12:18:10,443 ProgressMeter - chr12:60381241 2.01e+09 10.5 m 0.0 s 65.0% 16.2 m 5.7 m 
INFO 12:18:40,445 ProgressMeter - chr13:27611641 2.11e+09 11.0 m 0.0 s 68.2% 16.1 m 5.1 m 
INFO 12:19:10,446 ProgressMeter - chr14:15346101 2.20e+09 11.5 m 0.0 s 71.6% 16.1 m 4.6 m 
INFO 12:19:40,456 ProgressMeter - chr15:9565601 2.31e+09 12.0 m 0.0 s 74.8% 16.0 m 4.0 m 
INFO 12:20:10,457 ProgressMeter - chr16:5380553 2.42e+09 12.5 m 0.0 s 78.0% 16.0 m 3.5 m 
INFO 12:20:40,459 ProgressMeter - chr17:7484705 2.51e+09 13.0 m 0.0 s 81.0% 16.0 m 3.0 m 
INFO 12:21:10,460 ProgressMeter - chr18:12533677 2.59e+09 13.5 m 0.0 s 83.8% 16.1 m 2.6 m 
INFO 12:21:40,462 ProgressMeter - chr19:34306113 2.69e+09 14.0 m 0.0 s 87.0% 16.1 m 2.1 m 
INFO 12:22:10,463 ProgressMeter - chr20:55319685 2.77e+09 14.5 m 0.0 s 89.6% 16.2 m 100.0 s 
INFO 12:22:40,465 ProgressMeter - chr22:41605677 2.87e+09 15.0 m 0.0 s 92.8% 16.2 m 70.0 s 
INFO 12:23:10,466 ProgressMeter - chrX:84912589 2.97e+09 15.5 m 0.0 s 95.8% 16.2 m 40.0 s 
INFO 12:23:40,468 ProgressMeter - chrY:30850957 3.07e+09 16.0 m 0.0 s 99.1% 16.1 m 8.0 s 
INFO 12:23:47,504 ProgressMeter - done 3.10e+09 16.1 m 0.0 s 100.0% 16.1 m 0.0 s 
INFO 12:23:47,505 ProgressMeter - Total runtime 967.10 secs, 16.12 min, 0.27 hours 
INFO 12:23:47,591 MicroScheduler - 1390162 reads were filtered out during the traversal out of approximately 5682566 total reads (24.46%) 
INFO 12:23:47,591 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO 12:23:47,592 MicroScheduler - -> 51548 reads (0.91% of total) failing BadMateFilter 
INFO 12:23:47,592 MicroScheduler - -> 352814 reads (6.21% of total) failing DuplicateReadFilter 
INFO 12:23:47,592 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
INFO 12:23:47,592 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO 12:23:47,592 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
INFO 12:23:47,592 MicroScheduler - -> 985800 reads (17.35% of total) failing MappingQualityZeroFilter 
INFO 12:23:47,593 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter 
INFO 12:23:47,593 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter 
INFO 12:23:47,593 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter 
INFO 12:23:49,381 GATKRunReport - Uploaded run statistics report to AWS S3

Regards


Created 2013-09-08 01:15:58 | Updated | Tags: indels filters
Comments (8)

Hi, I am trying to filter the indels using GenomeAnalysisTK.jar -l INFO -T VariantFiltration -R reference.fa -V raw_indels.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 ||ReadPosRankSum < -20.0" --filterName "my_indels_filter" -o filtered_indels.vcf

But I donot get the filtered file, instead i get the same indels as before, with no error message, please guide me if I doing in right way.

Here is the output that I get:

chr1 2379 . A AGAG 1359.54 my_indels_filter AC=4;AF=0.500;AN=8;BaseQRankSum=5.734;DP=67;FS=0.000;HaplotypeScore=230.3405;MLEAC=4;MLEAF=0.500;MQ=22.94;MQ0=4;MQRankSum=2.033;QD=20.29;ReadPosRankSum=3.432;SB=-1.476e-03 GT:AD:DP:GQ:PL 0/1:15,11:17:99:567,0,305 0/1:10,4:12:99:207,0,411 0/1:9,4:9:99:205,0,252 0/1:5,8:10:35:432,0,35 chr1 2414 . C CCCA 91.56 my_indels_filter AC=5;AF=0.625;AN=8;BaseQRankSum=4.234;DP=43;FS=0.000;HaplotypeScore=151.6242;MLEAC=5;MLEAF=0.625;MQ=23.55;MQ0=5;MQRankSum=-1.458;QD=18.87;ReadPosRankSum=-1.129;SB=-1.476e-03 GT:AD:DP:GQ:PL 0/1:9,3:10:99:276,0,262 0/1:3,1:4:56:56,0,122 0/1:12,2:7:99:139,0,241 1/1:0,2:9:24:395,24,0