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MuTect2 tumor only mode: empty VCFs

Hello,

I am trying to run Mutect2 in tumor only mode without a matching normal. However, when I did this, MuTect2 produced output VCFs that had a full header, but had no variant calls.

Here is a sample command that I ran to produce variant calls for chromosome 1:
module load gatk/3.5.0; java -Xmx10g -Djava.io.tmpdir=$TMP -jar GenomeAnalysisTK.jar -T MuTect2 -R $REFERENCE_GENOME_FA --dbsnp $DBSNP_VCF --cosmic $COSMIC_VCF -dt NONE --input_file:tumor $TUMOR_BAM --intervals chr1:1-249250621 -o $OUTPUT_VCF

Note: I ran a similar command to this (same input files, etc.) using MuTect v1.1.4 and it produced a complete VCF.

Can you please explain if there is anything I need to change?

Thank you,
Jeremy

Tagged:

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No, that should work. Can you confirm that this also happens if you remove -dt NONE from your command? Also, can you tell me how long it took to run this and what was the console output?

  • JeremyAdamsJeremyAdams OICRMember

    I ran the command on chr1 with the -dt NONE flag on and off.

    The same output (absence of variants) occurred without the -dt NONE flag.

    With the -dt NONE flag -> runtime was 89 minutes
    Without the -dt NONE flag -> runtime was 72 minutes

    Also, the console output for the run without the -dt NONE flag is below:

    Welcome to java/1.8.0_45
    Welcome to gatk/3.5.0
    INFO 12:46:58,826 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:46:58,829 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
    INFO 12:46:58,829 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 12:46:58,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 12:46:58,832 HelpFormatter - Program Args: -T MuTect2 -R /oicr/data/reference/genomes/homo_sapiens_mc/UCSC/hg19_random/Genomic/references/fasta/hg19_random.fa -I:tumor /.mounts/labs/prod/archive/projects/steinlab/GECCO/data/bam/bwamem_bfmc/GECCO_6000_Ly_R_PE_255_TS.merged.sorted.filter.bam --dbsnp /.mounts/labs/PDE/data/MutectStrelka/dbSNP/dbsnp_138.hg19.leftAligned.vcf.gz --cosmic /.mounts/labs/PDE/data/MutectStrelka/cosmic/hg19_cosmic_v54_120711.vcf --artifact_detection_mode --intervals chr1:1-249250621 -o /.mounts/labs/prod/archive/projects/steinlab/GECCO/data/vcf/bwamem/somatic/panel_of_normals_test/mutect2.vcf
    INFO 12:46:58,838 HelpFormatter - Executing as [email protected] on Linux 3.14.27-oicr2.0 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
    INFO 12:46:58,838 HelpFormatter - Date/Time: 2016/01/08 12:46:58
    INFO 12:46:58,838 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:46:58,838 HelpFormatter - --------------------------------------------------------------------------------
    INFO 12:46:59,374 GenomeAnalysisEngine - Strictness is SILENT
    INFO 12:46:59,458 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO 12:46:59,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 12:46:59,506 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
    INFO 12:46:59,853 IntervalUtils - Processing 249250621 bp from intervals
    WARN 12:46:59,858 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
    INFO 12:46:59,957 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
    INFO 12:47:00,029 GenomeAnalysisEngine - Done preparing for traversal
    INFO 12:47:00,030 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 12:47:00,030 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 12:47:00,030 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
    INFO 12:47:00,113 MuTect2 - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
    Using SSE4.1 accelerated implementation of PairHMM
    INFO 12:47:02,986 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
    INFO 12:47:02,987 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
    INFO 12:47:30,033 ProgressMeter - chr1:1116439 0.0 30.0 s 49.6 w 0.4% 111.6 m 111.1 m
    INFO 12:48:00,034 ProgressMeter - chr1:6258054 0.0 60.0 s 99.2 w 2.5% 39.8 m 38.8 m
    INFO 12:48:30,035 ProgressMeter - chr1:11561338 0.0 90.0 s 148.8 w 4.6% 32.3 m 30.8 m
    INFO 12:49:00,036 ProgressMeter - chr1:11561801 0.0 120.0 s 198.4 w 4.6% 43.1 m 41.1 m
    INFO 12:49:30,038 ProgressMeter - chr1:11563019 0.0 2.5 m 248.0 w 4.6% 53.9 m 51.4 m
    INFO 12:50:00,039 ProgressMeter - chr1:11575632 0.0 3.0 m 297.6 w 4.6% 64.6 m 61.6 m
    INFO 12:50:30,040 ProgressMeter - chr1:11577853 0.0 3.5 m 347.2 w 4.6% 75.3 m 71.8 m
    INFO 12:51:00,041 ProgressMeter - chr1:11579756 0.0 4.0 m 396.8 w 4.6% 86.1 m 82.1 m
    INFO 12:51:30,042 ProgressMeter - chr1:11581092 0.0 4.5 m 446.4 w 4.6% 96.8 m 92.3 m
    INFO 12:52:00,044 ProgressMeter - chr1:11585511 0.0 5.0 m 496.1 w 4.6% 107.6 m 102.6 m
    INFO 12:52:30,045 ProgressMeter - chr1:11589878 0.0 5.5 m 545.7 w 4.6% 118.3 m 112.8 m
    INFO 12:53:00,046 ProgressMeter - chr1:11591903 0.0 6.0 m 595.3 w 4.7% 2.2 h 2.1 h
    INFO 12:53:30,047 ProgressMeter - chr1:11595368 0.0 6.5 m 644.9 w 4.7% 2.3 h 2.2 h
    INFO 12:54:00,056 ProgressMeter - chr1:11597074 0.0 7.0 m 694.5 w 4.7% 2.5 h 2.4 h
    INFO 12:54:30,058 ProgressMeter - chr1:16874478 0.0 7.5 m 744.1 w 6.8% 110.8 m 103.3 m
    INFO 12:55:00,059 ProgressMeter - chr1:24078650 0.0 8.0 m 793.7 w 9.7% 82.8 m 74.8 m
    INFO 12:55:30,060 ProgressMeter - chr1:27057904 0.0 8.5 m 843.3 w 10.9% 78.3 m 69.8 m
    INFO 12:56:00,061 ProgressMeter - chr1:27087873 0.0 9.0 m 892.9 w 10.9% 82.8 m 73.8 m
    INFO 12:56:30,063 ProgressMeter - chr1:27088188 0.0 9.5 m 942.5 w 10.9% 87.4 m 77.9 m
    INFO 12:57:00,064 ProgressMeter - chr1:27089172 0.0 10.0 m 992.1 w 10.9% 92.0 m 82.0 m
    INFO 12:57:30,065 ProgressMeter - chr1:27092997 0.0 10.5 m 1041.7 w 10.9% 96.6 m 86.1 m
    INFO 12:58:00,066 ProgressMeter - chr1:27092997 0.0 11.0 m 1091.3 w 10.9% 101.2 m 90.2 m
    INFO 12:58:30,068 ProgressMeter - chr1:27097975 0.0 11.5 m 1140.9 w 10.9% 105.8 m 94.3 m
    INFO 12:59:00,069 ProgressMeter - chr1:27097975 0.0 12.0 m 1190.5 w 10.9% 110.4 m 98.4 m
    INFO 12:59:30,070 ProgressMeter - chr1:27099256 0.0 12.5 m 1240.1 w 10.9% 115.0 m 102.5 m
    INFO 13:00:00,071 ProgressMeter - chr1:27101095 0.0 13.0 m 1289.8 w 10.9% 119.6 m 106.6 m
    INFO 13:00:30,072 ProgressMeter - chr1:27102382 0.0 13.5 m 1339.4 w 10.9% 2.1 h 110.7 m
    INFO 13:01:00,074 ProgressMeter - chr1:27105793 0.0 14.0 m 1389.0 w 10.9% 2.1 h 114.7 m
    INFO 13:01:30,075 ProgressMeter - chr1:27106607 0.0 14.5 m 1438.6 w 10.9% 2.2 h 118.8 m
    INFO 13:02:00,076 ProgressMeter - chr1:27107542 0.0 15.0 m 1488.2 w 10.9% 2.3 h 2.0 h
    INFO 13:02:30,077 ProgressMeter - chr1:40383122 0.0 15.5 m 1537.8 w 16.2% 95.7 m 80.2 m
    INFO 13:03:00,078 ProgressMeter - chr1:45796492 0.0 16.0 m 1587.4 w 18.4% 87.1 m 71.1 m
    INFO 13:03:30,080 ProgressMeter - chr1:45797991 0.0 16.5 m 1637.0 w 18.4% 89.8 m 73.3 m
    INFO 13:04:00,081 ProgressMeter - chr1:45799523 0.0 17.0 m 1686.6 w 18.4% 92.5 m 75.5 m
    INFO 13:04:30,082 ProgressMeter - chr1:45800364 0.0 17.5 m 1736.2 w 18.4% 95.2 m 77.7 m
    INFO 13:05:00,083 ProgressMeter - chr1:46290451 0.0 18.0 m 1785.8 w 18.6% 96.9 m 78.9 m
    INFO 13:05:30,085 ProgressMeter - chr1:46331056 0.0 18.5 m 1835.4 w 18.6% 99.5 m 81.0 m
    INFO 13:06:00,133 ProgressMeter - chr1:46379802 0.0 19.0 m 1885.1 w 18.6% 102.1 m 83.1 m
    INFO 13:06:30,134 ProgressMeter - chr1:46383244 0.0 19.5 m 1934.7 w 18.6% 104.8 m 85.3 m
    INFO 13:07:00,135 ProgressMeter - chr1:46425333 0.0 20.0 m 1984.3 w 18.6% 107.4 m 87.4 m
    INFO 13:07:30,137 ProgressMeter - chr1:46425333 0.0 20.5 m 2033.9 w 18.6% 110.1 m 89.6 m
    INFO 13:08:00,138 ProgressMeter - chr1:46463663 0.0 21.0 m 2083.5 w 18.6% 112.7 m 91.7 m
    INFO 13:08:30,139 ProgressMeter - chr1:46472106 0.0 21.5 m 2133.1 w 18.6% 115.3 m 93.8 m
    INFO 13:09:00,141 ProgressMeter - chr1:46474287 0.0 22.0 m 2182.7 w 18.6% 118.0 m 96.0 m
    INFO 13:09:30,142 ProgressMeter - chr1:46485526 0.0 22.5 m 2232.3 w 18.7% 2.0 h 98.1 m
    INFO 13:10:00,143 ProgressMeter - chr1:46487842 0.0 23.0 m 2281.9 w 18.7% 2.1 h 100.3 m
    INFO 13:10:30,144 ProgressMeter - chr1:46488830 0.0 23.5 m 2331.5 w 18.7% 2.1 h 102.5 m
    INFO 13:11:00,145 ProgressMeter - chr1:46489862 0.0 24.0 m 2381.1 w 18.7% 2.1 h 104.7 m
    INFO 13:11:30,147 ProgressMeter - chr1:46491675 0.0 24.5 m 2430.7 w 18.7% 2.2 h 106.8 m
    INFO 13:12:00,148 ProgressMeter - chr1:46491675 0.0 25.0 m 2480.4 w 18.7% 2.2 h 109.0 m
    INFO 13:12:30,149 ProgressMeter - chr1:46495444 0.0 25.5 m 2530.0 w 18.7% 2.3 h 111.2 m
    INFO 13:13:00,150 ProgressMeter - chr1:46495444 0.0 26.0 m 2579.6 w 18.7% 2.3 h 113.4 m
    INFO 13:13:30,152 ProgressMeter - chr1:46496619 0.0 26.5 m 2629.2 w 18.7% 2.4 h 115.6 m
    INFO 13:14:00,153 ProgressMeter - chr1:46497358 0.0 27.0 m 2678.8 w 18.7% 2.4 h 117.7 m
    INFO 13:14:30,154 ProgressMeter - chr1:46498611 0.0 27.5 m 2728.4 w 18.7% 2.5 h 119.9 m
    INFO 13:15:00,156 ProgressMeter - chr1:46500633 0.0 28.0 m 2778.0 w 18.7% 2.5 h 2.0 h
    INFO 13:15:30,157 ProgressMeter - chr1:46500977 0.0 28.5 m 2827.6 w 18.7% 2.5 h 2.1 h
    INFO 13:16:00,183 ProgressMeter - chr1:49000062 0.0 29.0 m 2877.2 w 19.7% 2.5 h 118.5 m
    INFO 13:16:30,184 ProgressMeter - chr1:49005606 0.0 29.5 m 2926.8 w 19.7% 2.5 h 2.0 h
    INFO 13:17:00,185 ProgressMeter - chr1:49056838 0.0 30.0 m 2976.4 w 19.7% 2.5 h 2.0 h
    INFO 13:17:30,187 ProgressMeter - chr1:49129117 0.0 30.5 m 3026.1 w 19.7% 2.6 h 2.1 h
    INFO 13:18:00,188 ProgressMeter - chr1:49129117 0.0 31.0 m 3075.7 w 19.7% 2.6 h 2.1 h
    INFO 13:18:30,189 ProgressMeter - chr1:49333102 0.0 31.5 m 3125.3 w 19.8% 2.7 h 2.1 h
    INFO 13:19:00,190 ProgressMeter - chr1:50163328 0.0 32.0 m 3174.9 w 20.1% 2.7 h 2.1 h
    INFO 13:19:30,192 ProgressMeter - chr1:50489712 0.0 32.5 m 3224.5 w 20.3% 2.7 h 2.1 h
    INFO 13:20:00,193 ProgressMeter - chr1:57192486 0.0 33.0 m 3274.1 w 22.9% 2.4 h 110.8 m
    INFO 13:20:30,194 ProgressMeter - chr1:85736812 0.0 33.5 m 3323.7 w 34.4% 97.4 m 63.9 m
    INFO 13:21:00,195 ProgressMeter - chr1:97544815 0.0 34.0 m 3373.3 w 39.1% 86.9 m 52.9 m
    INFO 13:21:30,196 ProgressMeter - chr1:97548126 0.0 34.5 m 3422.9 w 39.1% 88.2 m 53.7 m
    INFO 13:22:00,197 ProgressMeter - chr1:97548126 0.0 35.0 m 3472.5 w 39.1% 89.4 m 54.4 m
    INFO 13:22:30,199 ProgressMeter - chr1:97659093 0.0 35.5 m 3522.1 w 39.2% 90.6 m 55.1 m
    INFO 13:23:00,200 ProgressMeter - chr1:97771120 0.0 36.0 m 3571.7 w 39.2% 91.8 m 55.8 m
    INFO 13:23:30,201 ProgressMeter - chr1:97772087 0.0 36.5 m 3621.3 w 39.2% 93.0 m 56.5 m
    INFO 13:24:00,202 ProgressMeter - chr1:97981709 0.0 37.0 m 3670.9 w 39.3% 94.1 m 57.1 m
    INFO 13:24:30,203 ProgressMeter - chr1:98039726 0.0 37.5 m 3720.5 w 39.3% 95.3 m 57.8 m
    INFO 13:25:00,204 ProgressMeter - chr1:98059145 0.0 38.0 m 3770.1 w 39.3% 96.6 m 58.6 m
    INFO 13:25:30,206 ProgressMeter - chr1:98145024 0.0 38.5 m 3819.7 w 39.4% 97.8 m 59.3 m
    INFO 13:26:00,207 ProgressMeter - chr1:98165318 0.0 39.0 m 3869.3 w 39.4% 99.0 m 60.0 m
    INFO 13:26:30,208 ProgressMeter - chr1:98187352 0.0 39.5 m 3918.9 w 39.4% 100.3 m 60.8 m
    INFO 13:27:00,210 ProgressMeter - chr1:98293981 0.0 40.0 m 3968.6 w 39.4% 101.4 m 61.4 m
    INFO 13:27:30,211 ProgressMeter - chr1:98386706 0.0 40.5 m 4018.2 w 39.5% 102.6 m 62.1 m
    INFO 13:28:00,212 ProgressMeter - chr1:100534414 0.0 41.0 m 4067.8 w 40.3% 101.6 m 60.6 m
    INFO 13:28:30,213 ProgressMeter - chr1:115251422 0.0 41.5 m 4117.4 w 46.2% 89.8 m 48.3 m
    INFO 13:29:00,214 ProgressMeter - chr1:115256824 0.0 42.0 m 4167.0 w 46.2% 90.8 m 48.8 m
    INFO 13:29:30,216 ProgressMeter - chr1:117087185 0.0 42.5 m 4216.6 w 47.0% 90.5 m 48.0 m
    INFO 13:30:00,225 ProgressMeter - chr1:120053489 0.0 43.0 m 4266.2 w 48.2% 89.3 m 46.3 m
    INFO 13:30:30,226 ProgressMeter - chr1:147083936 0.0 43.5 m 4315.8 w 59.0% 73.7 m 30.2 m
    INFO 13:31:00,227 ProgressMeter - chr1:147086767 0.0 44.0 m 4365.4 w 59.0% 74.6 m 30.6 m
    INFO 13:31:30,229 ProgressMeter - chr1:147087902 0.0 44.5 m 4415.0 w 59.0% 75.4 m 30.9 m
    INFO 13:32:00,230 ProgressMeter - chr1:147090862 0.0 45.0 m 4464.6 w 59.0% 76.3 m 31.3 m
    INFO 13:32:30,231 ProgressMeter - chr1:147091974 0.0 45.5 m 4514.2 w 59.0% 77.1 m 31.6 m
    INFO 13:33:00,232 ProgressMeter - chr1:147093022 0.0 46.0 m 4563.8 w 59.0% 77.9 m 31.9 m
    INFO 13:33:30,233 ProgressMeter - chr1:147095933 0.0 46.5 m 4613.4 w 59.0% 78.8 m 32.3 m
    INFO 13:34:00,234 ProgressMeter - chr1:147096910 0.0 47.0 m 4663.0 w 59.0% 79.6 m 32.6 m
    INFO 13:34:30,235 ProgressMeter - chr1:152080479 0.0 47.5 m 4712.6 w 61.0% 77.8 m 30.3 m
    INFO 13:35:00,237 ProgressMeter - chr1:152082275 0.0 48.0 m 4762.2 w 61.0% 78.7 m 30.7 m
    INFO 13:35:30,238 ProgressMeter - chr1:152083659 0.0 48.5 m 4811.9 w 61.0% 79.5 m 31.0 m
    INFO 13:36:00,239 ProgressMeter - chr1:152085217 0.0 49.0 m 4861.5 w 61.0% 80.3 m 31.3 m
    INFO 13:36:30,240 ProgressMeter - chr1:152086790 0.0 49.5 m 4911.1 w 61.0% 81.1 m 31.6 m
    INFO 13:37:00,249 ProgressMeter - chr1:152086790 0.0 50.0 m 4960.7 w 61.0% 81.9 m 31.9 m
    INFO 13:37:30,250 ProgressMeter - chr1:156715400 0.0 50.5 m 5010.3 w 62.9% 80.3 m 29.8 m
    INFO 13:38:00,251 ProgressMeter - chr1:156715400 0.0 51.0 m 5059.9 w 62.9% 81.1 m 30.1 m
    INFO 13:38:30,252 ProgressMeter - chr1:169610133 0.0 51.5 m 5109.5 w 68.0% 75.7 m 24.2 m
    INFO 13:39:00,253 ProgressMeter - chr1:186283483 0.0 52.0 m 5159.1 w 74.7% 69.6 m 17.6 m
    INFO 13:39:30,254 ProgressMeter - chr1:186286952 0.0 52.5 m 5208.7 w 74.7% 70.2 m 17.7 m
    INFO 13:40:00,257 ProgressMeter - chr1:186287878 0.0 53.0 m 5258.3 w 74.7% 70.9 m 17.9 m
    INFO 13:40:30,258 ProgressMeter - chr1:186291937 0.0 53.5 m 5307.9 w 74.7% 71.6 m 18.1 m
    INFO 13:41:00,259 ProgressMeter - chr1:186296881 0.0 54.0 m 5357.5 w 74.7% 72.2 m 18.2 m
    INFO 13:41:30,260 ProgressMeter - chr1:186303894 0.0 54.5 m 5407.1 w 74.7% 72.9 m 18.4 m
    INFO 13:42:00,261 ProgressMeter - chr1:186304756 0.0 55.0 m 5456.7 w 74.7% 73.6 m 18.6 m
    INFO 13:42:30,262 ProgressMeter - chr1:186306049 0.0 55.5 m 5506.3 w 74.7% 74.3 m 18.8 m
    INFO 13:43:00,263 ProgressMeter - chr1:186306475 0.0 56.0 m 5555.9 w 74.7% 74.9 m 18.9 m
    INFO 13:43:30,264 ProgressMeter - chr1:186309124 0.0 56.5 m 5605.5 w 74.7% 75.6 m 19.1 m
    INFO 13:44:00,265 ProgressMeter - chr1:186310745 0.0 57.0 m 5655.2 w 74.7% 76.3 m 19.3 m
    INFO 13:44:30,266 ProgressMeter - chr1:186313430 0.0 57.5 m 5704.8 w 74.7% 76.9 m 19.4 m
    INFO 13:45:00,267 ProgressMeter - chr1:186314962 0.0 58.0 m 5754.4 w 74.8% 77.6 m 19.6 m
    INFO 13:45:30,268 ProgressMeter - chr1:186315555 0.0 58.5 m 5804.0 w 74.8% 78.3 m 19.8 m
    INFO 13:46:00,269 ProgressMeter - chr1:186316739 0.0 59.0 m 5853.6 w 74.8% 78.9 m 19.9 m
    INFO 13:46:30,271 ProgressMeter - chr1:186321355 0.0 59.5 m 5903.2 w 74.8% 79.6 m 20.1 m
    INFO 13:47:00,272 ProgressMeter - chr1:186326853 0.0 60.0 m 5952.8 w 74.8% 80.3 m 20.3 m
    INFO 13:47:30,273 ProgressMeter - chr1:186327989 0.0 60.5 m 6002.4 w 74.8% 80.9 m 20.4 m
    INFO 13:48:00,274 ProgressMeter - chr1:186329759 0.0 61.0 m 6052.0 w 74.8% 81.6 m 20.6 m
    INFO 13:48:30,275 ProgressMeter - chr1:186331215 0.0 61.5 m 6101.6 w 74.8% 82.3 m 20.8 m
    INFO 13:49:00,276 ProgressMeter - chr1:186337341 0.0 62.0 m 6151.2 w 74.8% 82.9 m 20.9 m
    INFO 13:49:30,277 ProgressMeter - chr1:186342878 0.0 62.5 m 6200.8 w 74.8% 83.6 m 21.1 m
    INFO 13:50:00,279 ProgressMeter - chr1:186345136 0.0 63.0 m 6250.4 w 74.8% 84.3 m 21.3 m
    INFO 13:50:30,280 ProgressMeter - chr1:197091600 0.0 63.5 m 6300.0 w 79.1% 80.3 m 16.8 m
    INFO 13:51:00,281 ProgressMeter - chr1:201981481 0.0 64.0 m 6349.6 w 81.0% 79.0 m 15.0 m
    INFO 13:51:30,282 ProgressMeter - chr1:201982499 0.0 64.5 m 6399.2 w 81.0% 79.6 m 15.1 m
    INFO 13:52:00,283 ProgressMeter - chr1:201982499 0.0 65.0 m 6448.8 w 81.0% 80.2 m 15.2 m
    INFO 13:52:30,291 ProgressMeter - chr1:201984522 0.0 65.5 m 6498.4 w 81.0% 80.8 m 15.3 m
    INFO 13:53:00,292 ProgressMeter - chr1:201984522 0.0 66.0 m 6548.1 w 81.0% 81.4 m 15.4 m
    INFO 13:53:30,293 ProgressMeter - chr1:227751656 0.0 66.5 m 6597.7 w 91.4% 72.8 m 6.3 m
    INFO 13:54:00,294 ProgressMeter - chr1:227751656 0.0 67.0 m 6647.3 w 91.4% 73.3 m 6.3 m
    INFO 13:54:30,295 ProgressMeter - chr1:227834499 0.0 67.5 m 6696.9 w 91.4% 73.8 m 6.3 m
    INFO 13:55:00,297 ProgressMeter - chr1:227842735 0.0 68.0 m 6746.5 w 91.4% 74.4 m 6.4 m
    INFO 13:55:30,298 ProgressMeter - chr1:227843636 0.0 68.5 m 6796.1 w 91.4% 74.9 m 6.4 m
    INFO 13:56:00,299 ProgressMeter - chr1:233489731 0.0 69.0 m 6845.7 w 93.7% 73.7 m 4.7 m
    INFO 13:56:30,300 ProgressMeter - chr1:233498094 0.0 69.5 m 6895.3 w 93.7% 74.2 m 4.7 m
    INFO 13:57:00,301 ProgressMeter - chr1:233514965 0.0 70.0 m 6944.9 w 93.7% 74.7 m 4.7 m
    INFO 13:57:30,302 ProgressMeter - chr1:233515660 0.0 70.5 m 6994.5 w 93.7% 75.3 m 4.8 m
    INFO 13:58:00,303 ProgressMeter - chr1:233515660 0.0 71.0 m 7044.1 w 93.7% 75.8 m 4.8 m
    INFO 13:58:30,304 ProgressMeter - chr1:233518540 0.0 71.5 m 7093.7 w 93.7% 76.3 m 4.8 m
    INFO 13:59:00,305 ProgressMeter - chr1:233518540 0.0 72.0 m 7143.3 w 93.7% 76.9 m 4.9 m
    INFO 13:59:18,907 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.636457736
    INFO 13:59:18,908 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3733.8087024270003
    INFO 13:59:18,909 MuTect2 - Ran local assembly on 0 active regions
    INFO 13:59:18,924 ProgressMeter - done 2.49250621E8 72.3 m 17.0 s 100.0% 72.3 m 0.0 s
    INFO 13:59:18,924 ProgressMeter - Total runtime 4338.89 secs, 72.31 min, 1.21 hours
    INFO 13:59:18,925 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 622372 total reads (0.00%)
    INFO 13:59:18,925 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
    INFO 13:59:18,926 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
    INFO 13:59:18,926 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
    INFO 13:59:18,927 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
    INFO 13:59:18,927 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
    INFO 13:59:18,927 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
    INFO 13:59:18,928 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
    INFO 13:59:19,670 GATKRunReport - Uploaded run statistics report to AWS S3

  • JeremyAdamsJeremyAdams OICRMember

    Great, thank you

  • bracha25bracha25 Member

    When do you expect the bug to be fixed? Also, if I do not supply a whole-exome intervals list, does it change the statistics of variant calling to that of whole genome sequencing?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @bracha25,

    We're going to push for this to be prioritized but it could still be a couple of weeks before we have a fix ready to share.

    Supplying a list of intervals does not change the statistical calculations, it only restricts analysis to those intervals. So generally speaking for the positions within those intervals, the results should be the same or equivalent (marginal differences can occur to differences in downsampling in high-depth regions).

    Note however that positions on the very ends of the intervals can be affected by edge effects, so when you supply intervals, we do recommend padding the intervals with up to 100 bases on either side, which can be done with the engine argument -ip.

  • bracha25bracha25 Member
    edited January 2016

    Thank you. I did forget to ask if eliminating the intervals list will allow me to avoid the bug? If not, can you recommend an alternative way to call indels that is compatible with MuTect1?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I don't think so, but you can try.

    The original MuTect does not have any indel calling capability.

  • rshahirshahi BrusselMember

    @bracha25 I have tried it, it did not work.

  • bracha25bracha25 Member

    Thanks Geraldine, I know that MuTect1 does not call indels. I would like to do so, with another tool that will give similar output. Will HaplotypeCaller be a good choice (in our case time is of the essence, so we may not be able to wait for the fix)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    If you mean, is it ok to create your PoN with HaplotypeCaller, the answer is that it's not ideal (because it won't perform the same artifact-canceling role, only the germline-variant-canceling) but it's better than nothing.

  • bracha25bracha25 Member

    Thank you! I appreciate your quick responses.

  • sboylesboyle Bay Area, CAMember

    Has the tumor only mode bug been fixed or do you have a tentative timeline for what it will be addressed?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @sboyle The bug we have been discussing here has to do with PoN creation, not running on tumors only.

    This bug has indeed been fixed in the nightly builds.

  • sboylesboyle Bay Area, CAMember
    edited January 2016

    @Geraldine_VdAuwera : Thanks! Then Mutect2 can be run in tumor only mode as well as tumor-normal, correct?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It can be done, technically speaking, but we consider that it's not a good experimental design.

  • manon_sourdeixmanon_sourdeix FranceMember

    Hi @Geraldine_VdAuwera
    I tried MuTect2 in tumor only mode last night but the vcf is empty just like @sboyle

    My version is 3.5-0. Should I be re-downloading it ? Any suggestion how to solve that issue ?

    Thanks a lot.
    Manon

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Yes you can try the latest nightly build (available from the downloads section).

  • elielliseliellis FlorenceMember

    Hi @Geraldine_VdAuwera,
    I tried MuTect2 in tumor only mode yesterday with the latest version (downloaded yesterday) but the vcf file is still empty.
    Could you help me?
    Thanks
    Eliellis

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @eliellis
    Hi Eliellis,

    Can you post the exact command you ran?

    Thanks,
    Sheila

  • manon_sourdeixmanon_sourdeix FranceMember

    @eliellis got the same but you should download the lates nightly build and then it works fine

  • elielliseliellis FlorenceMember

    we have tried with the nightly version and now it works !
    Thanks

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @manon_sourdeix
    Hi Manon,

    Thanks for catching Eliellis was using the latest stable version and not the latest nightly! :smiley:

    Sheila

  • luj01luj01 Wilmington, DEMember

    Hello, I had the same results with empty vcf using GATK-3.5 downloaded on April 25. Has the bug been fixed in the latest stable or nightly build? It took me 7 hrs to see whether it works or not. How to speed up if you have hundreds of GB RAMs and a quite number of CPUs? thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Yes it's fixed in the nightly builds.

    You can always do a test run on a short region with -L to see if it works without waiting a long time.
  • luj01luj01 Wilmington, DEMember

    I downloaded May 26th and May 8th nightly build. None of them worked.
    Error is
    Exception in thread "main" java.lang.UnsupportedClassVersionError: htsjdk/tribble/TribbleException : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at java.lang.Class.getDeclaredMethods0(Native Method)
    at java.lang.Class.privateGetDeclaredMethods(Class.java:2625)
    at java.lang.Class.getMethod0(Class.java:2866)
    at java.lang.Class.getMethod(Class.java:1676)
    at sun.launcher.LauncherHelper.getMainMethod(LauncherHelper.java:494)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:486)
    My java version is 1.7.0_8. Is there any nightly build supporting java 1.7? thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No, the latest nightlies are all java 1.8. You'll need to change your java version.

  • mikitebamikiteba MeldolaMember

    Hello, I had the same results with empty vcf using GATK-3.5 downloaded today and running with java 1.8. Could you help me?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mikiteba
    Hi,

    Try the latest version (3.6).

    -Sheila

  • Lyon0804Lyon0804 Hangzhou, ChinaMember

    @Sheila @Geraldine_VdAuwera

    Hi, I use GATK-3.6 MuTect2 calling tumor-only sample, but it seems that all the record's "GT" are "0/1", even though one of the allele depth is 0.
    For example:

    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:0,3579:1.00:1326:2253:0.630:0,99242:0:0
    GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:0,3113:1.00:1185:1928:0.381:0,85256:0:0

    Is there a bug?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Lyon0804
    Hi,

    Can you please post an IGV screenshot of the BAM file at that position? Also, please post the corresponding bamout file.

    Thanks,
    Sheila

  • mrs72mrs72 CamMember

    ~Update on this ~

    Hi Sheila and Geraldine,

    Thanks for tracking down and fixing the bug!

    I had experienced similar problems with an empty VCF as the other users who have posted above. Now updated from GATK 3.5 to 3.6 version, under java environment 1.8.0 - and the latter works.

    Cheers,
    Max

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