Tagged with #indel
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The answer depends on what tool we're talking about, and whether we're considering variant discovery or variant manipulation.

GATK variant manipulation tools are able to recognize the following types of alleles:

  • SNP (single nucleotide polymorphism)
  • INDEL (insertion/deletion)
  • MIXED (combination of SNPs and indels at a single position)
  • MNP (multi-nucleotide polymorphism, e.g. a dinucleotide substitution)
  • SYMBOLIC (generally, a very large allele or one that's fuzzy and not fully modeled; i.e. there's some event going on here but we don't know what exactly)

Of our two variant callers, UnifiedGenotyper is the more limited, as it only calls SNPs and indels, and does so separately (even if you run in calling mode BOTH, the program performs separate calling operations internally). The HaplotypeCaller is more sophisticated and calls different types of variants at the same time. So in addition to SNPs and indels, it is capable of emitting mixed records by default. It is also capable of emitting MNPs and symbolic alleles, but the modes to do so are not enabled by default and they are not part of our recommended best practices for the tool.

The GATK currently does not handle SVs (structural variations) or CNVs (copy number variations), but there are some third-party software packages built on top of GATK that provide this functionality. See GenomeSTRiP for SVs and XHMM for CNVs.

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Comments (1)


first of all thanks for the support offered here. But (sadly) I have an other two questions.

I used the FastaAlternateReferenceMaker to create a consesus sequence and it worked great. Here I have a question regarding a warning: "IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation". I do not get this warning. Which dictionary is needed here. Is this warning comming up, because I used .gz and .tbi compressed vcf-files?

And a furhter question regarding the creation of a consesus sequence. I`m unsure what to do in cases of heterozygous INDELs. What would you suggest to do? Skip them as they are only represented by one allele or include them in the consensus. Both seems to be incorrect. Do you know the general handling here?


Comments (2)


Can i use HaplotypeCaller to call the 454 indel? Can anyone share his/her idea?thanks.

Best, J

Comments (4)

Hello all,

I have narrowed down this issue to UG Indel caller. I am currently running UG will an additional 136 1000Genome individuals to be call at the same time my variants of interest. I run my SNP and Indel calls separate as per GATK best practices. But have noticed this issue only with my Indel calls.

This is the command I'm running:

java -Xmx32g -jar -Djava.io.tmpdir=/tmp/ /home/srynearson/GenomeAnalysisTK-nightly-oct/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /home/srynearson/cAPTUrE/references/human_g1k_v37.fasta -I [each of the 1000Genome .bam files] -I [each of my variants of interest .bam files] --num_threads 15 --standard_min_confidence_threshold_for_calling 30.0 --standard_min_confidence_threshold_for_emitting 30.0 --output_mode EMIT_VARIANTS_ONLY --num_cpu_threads_per_data_thread 2 --genotype_likelihoods_model INDEL

And this is the error I get:

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Somehow the requested coordinate is not covered by the read. Alignment 88304365 | 67S24M1D8M1S at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:574) at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:438) at org.broadinstitute.sting.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(ReadUtils.java:434) at org.broadinstitute.sting.gatk.walkers.annotator.BaseQualityRankSumTest.getElementForRead(BaseQualityRankSumTest.java:76) at org.broadinstitute.sting.gatk.walkers.annotator.RankSumTest.getElementForRead(RankSumTest.java:200) at org.broadinstitute.sting.gatk.walkers.annotator.RankSumTest.fillQualsFromLikelihoodMap(RankSumTest.java:179) at org.broadinstitute.sting.gatk.walkers.annotator.RankSumTest.annotate(RankSumTest.java:102) at org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:192) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateGenotypes(UnifiedGenotyperEngine.java:560) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotyperEngine.java:234) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367) at org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:724)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version nightly-2013-10-04-ge260355):
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 MESSAGE: Somehow the requested coordinate is not covered by the read. Alignment 88304365 | 67S24M1D8M1S
ERROR ------------------------------------------------------------------------------------------

I have confirmed prior files and the SNP file runs to completion.

Any ideas? Thanks!

Comments (4)

I have Ion Torrent data. I am trying to call a variant that I know to exist (confirmed with Sanger). In the position where there is the known indel, I have a depth of roughly 80-90 (in two different runs) and a of those between 20-23% of the reads have the insertion called. What parameters should I be adjusting to get this indel to call? I don't mind a large number of false positives.

I've tried several iterations that include indel realignment using known indels (1000G_phase1 and ills_and_1000G_gold_standard) and also excluding them. I have also tried iterations of setting these flags in UnifiedGenotyper:-stand_call_conf 30.0 -stand_emit_conf 0.0 --min_base_quality_score 0 -glm BOTH --dbsnp dbsnp_137.b37.vcf -nt -rf BadCigar -minIndelCnt 3 -minIndelFrac 0.15. I have also attempted to use HaplotypeCaller: -stand_call_conf 30.0 -stand_emit_conf 0.0 --dbsnp dbsnp_137.b37.vcf -rf BadCigar

Any suggestions would be great.

Comments (5)


I'm having problems understanding a GATK output VCF. I have read the VCF standard, but I'm obviously missing something.

I /think/ I understand how SNPs and short indels are represented, but clearly I do not. Below is an excerpt that illustrates sites which I do not understand. I suspect it may be something to do with GATK quality filters that I'm not understanding, or something about using EMIT_ALL_SITES...

The excerpt below was generated using

GATK -l INFO -I my.bam -R my.fa -T UnifiedGenotyper -S LENIENT -nt 8 --heterozygosity 0.1 -o test.vcf --genotype_likelihoods_model BOTH --min_base_quality_score 10 --output_mode EMIT_ALL_SITES -ploidy 2



    CH1 225 .   T   G   12.71   LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.978;DP=59;Dels=0.03;FS=0.000;HaplotypeScore=10.2840;MLEAC=1;MLEAF=0.500;MQ=70.25;MQ0=8;MQRankSum=-5.349;QD=0.22;ReadPosRankSum=-3.188 GT:AD:DP:GQ:PL  0/1:41,16:55:20:20,0,1435
    CH1 226 .   T   .   121.53  .   AN=2;DP=59;MQ=70.25;MQ0=8   GT:DP   0/0:43
    CH1 227 .   A   .   121.53  .   AN=2;DP=59;MQ=70.25;MQ0=8   GT:DP   0/0:43
    CH1 228 .   T   .   121.53  .   AN=2;DP=59;MQ=70.25;MQ0=8   GT:DP   0/0:43
    CH1 229 .   A   .   115.53  .   AN=2;DP=57;MQ=69.66;MQ0=8   GT:DP   0/0:38
    CH1 230 .   C   .   115.53  .   AN=2;DP=57;MQ=69.66;MQ0=8   GT:DP   0/0:38
    CH1 231 .   T   .   115.53  .   AN=2;DP=57;MQ=69.66;MQ0=8   GT:DP   0/0:36
    CH1 232 .   G   .   115.53  .   AN=2;DP=57;MQ=69.66;MQ0=8   GT:DP   0/0:36
    CH1 233 .   C   .   115.53  .   AN=2;DP=57;MQ=69.66;MQ0=8   GT:DP   0/0:37
    CH1 234 .   A   .   139.53  .   AN=2;DP=70;MQ=59.20;MQ0=14  GT:DP   0/0:63
    CH1 235 .   A   .   175.53  .   AN=2;DP=84;MQ=51.67;MQ0=15  GT:DP   0/0:79
    CH1 236 .   A   .   175.53  .   AN=2;DP=84;MQ=51.67;MQ0=15  GT:DP   0/0:79
    CH1 237 .   T   .   175.53  .   AN=2;DP=85;MQ=51.37;MQ0=16  GT:DP   0/0:80
    CH1 238 .   A   .   175.53  .   AN=2;DP=102;MQ=46.90;MQ0=28 GT:DP   0/0:97
    CH1 238 .   A   AGAAAGAAAGCTTGTA    83.73   .   AC=1;AF=0.500;AN=2;BaseQRankSum=6.172;DP=102;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=46.90;MQ0=0;MQRankSum=-6.190;QD=0.05;ReadPosRankSum=-5.733 GT:AD:DP:GQ:PL  0/1:27,25:57:99:121,0,4853
    CH1 239 .   A   .   175.53  .   AN=2;DP=102;MQ=46.90;MQ0=28 GT:DP   0/0:101
    CH1 240 .   T   .   175.53  .   AN=2;DP=102;MQ=46.90;MQ0=28 GT:DP   0/0:98
    CH1 241 .   A   .   169.53  .   AN=2;DP=108;MQ=44.14;MQ0=29 GT:DP   0/0:107
*    CH1    242 .   T   .   169.53  .   AN=2;DP=109;MQ=43.94;MQ0=29 GT:DP   0/0:103
*    CH1    242 .   T   .   118.27  .   AN=2;DP=109;MQ=43.94;MQ0=29 GT:AD:DP    0/0:27:55
*    CH1    243 .   C   .   172.53  .   AN=2;DP=110;MQ=43.76;MQ0=29 GT:DP   0/0:108
*    CH1    243 .   CTTTT   .   118.27  .   AN=2;DP=110;MQ=43.76;MQ0=29 GT:AD:DP    0/0:27:56
    CH1 244 .   T   .   91.53   .   AN=2;DP=110;MQ=43.76;MQ0=29 GT:DP   0/0:61
    CH1 245 .   T   .   91.53   .   AN=2;DP=110;MQ=43.76;MQ0=29 GT:DP   0/0:53
    CH1 246 .   T   .   73.53   .   AN=2;DP=110;MQ=43.76;MQ0=29 GT:DP   0/0:41
    CH1 247 .   T   .   91.53   .   AN=2;DP=110;MQ=43.76;MQ0=29 GT:DP   0/0:46
    CH1 248 .   A   .   172.53  .   AN=2;DP=116;MQ=42.61;MQ0=31 GT:DP   0/0:100
    CH1 249 .   A   .   172.53  .   AN=2;DP=116;MQ=42.61;MQ0=31 GT:DP   0/0:100
    CH1 250 .   T   .   172.53  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:DP   0/0:101
    CH1 251 .   T   .   169.53  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:DP   0/0:96
    CH1 251 .   T   .   118.27  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:AD:DP    0/0:27:56
    CH1 252 .   C   .   172.53  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:DP   0/0:113
    CH1 253 .   C   .   172.53  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:DP   0/0:110
    CH1 254 .   T   .   172.53  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:DP   0/0:111
    CH1 255 .   T   .   172.53  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:DP   0/0:111
    CH1 256 .   T   .   172.53  .   AN=2;DP=117;MQ=42.43;MQ0=32 GT:DP   0/0:111

Line 1 is a SNP
Lines 14 and 15 are an indel that I do understand
Lines 19 and 20 I do /not/ understand
Lines 21 and 22 I do /not/ understand

Comments (3)

Dear All,

Just thought I should report a possible small bug with SelectVariant --maxIndelSize as I think it's only filtering insertions greater than the given value and not deletions. Of course using JEXL expressions I can still get the variants I'm after...

Cheers, Laurent