Tagged with #variants
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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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1. What file formats do you support for variant callsets?

We support the Variant Call Format (VCF) for variant callsets. No other file formats are supported.

2. How can I know if my VCF file is valid?

VCFTools contains a validation tool that will allow you to verify it.

3. Are you planning to include any converters from different formats or allow different input formats than VCF?

No, we like VCF and we think it's important to have a good standard format. Multiplying formats just makes life hard for everyone, both developers and analysts.

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Comments (6)

Dear, GATK team, I have done raw snp and indel calling with UnifiedGenotyper following the command line below.

java -Xmx16g -jar GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -glm BOTH -R ucsc.hg19.fasta -T UnifiedGenotyper -I ERR031029.marked.realigned.fixed.recal.bam -I ERR031030.marked.realigned.fixed.recal.bam -D dbsnp_135.hg19.vcf -o ERR031030.raw.snps.indels.vcf -metrics snps.metrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000

After that, I did snp filteration using the following command lines.

java -Xmx8g -jar GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T SelectVariants --variant ERR031030.raw.snps.indels.vcf -o ERR031030.snpsonly.vcf -selectType SNP

java -Xmx8g -jar GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T SelectVariants --variant ERR031030.raw.snps.indels.vcf -o ERR031030.indelsonly.vcf -selectType INDEL

java -Xmx8g -jar GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T VariantRecalibrator -R ucsc.hg19.fasta -input ERR031030.snpsonly.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_phase1.indels.hg19.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_135.hg19.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ -mode SNP -recalFile ERR031030.snp.recal.vcf -tranchesFile ERR031030.snp.tranches.vcf -rscriptFile ERR031030.plots.R

java -Xmx8g -jar GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T ApplyRecalibration -input ERR031030.snpsonly.vcf -tranchesFile ERR031030.snp.tranches.vcf -recalFile ERR031030.snp.recal.vcf -o ERR031030.snps.filtered.vcf

java -Xmx16g -jar GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T VariantFiltration --variant ERR031030.snps.filtered.vcf -o ERR031030.final.filtered.vcf --filterName "Nov28filters && QD < 2.0 && ReadPosRankSum < -8.0 && MQ < 40.0 && FS > 60.0 && MQRandkSum < -12.5"  --filterExpression "HaplotypeScore > 13.0"

The filtered snp.vcf file came up, however, it seems it contains some problem.

chrM    311     .       T       C       429.19  Nov28filters **_&& QD < 2.0 && ReadPosRankSum < -8.0 && MQ < 40.0 && FS > 60.0 && MQRandkSum < -12.5;VQSRTrancheSNP99.90to100.00   AC=1;AF=0.250;AN=4;BaseQRankSum=-13.010;DP=2000;Dels=0.00;FS=50.500;HaplotypeScore=382.2016;MLEAC=1;MLEAF=0.250;MQ=50.86;MQ0=0;MQRankSum=1.458;QD=0.43;ReadPosRankSum=-10.687;VQSLOD=-6.143e+02;culprit=HaplotypeScore  GT:AD:DP:GQ:PL  0/0:634,353:949:99:0,232,7697   0/1:463,521:945:99:459,0,4190
chrM    410     .       A       T       64750.20        PASS    AC=4;AF=1.00;AN=4;DP=2000;Dels=0.00;FS=0.000;HaplotypeScore=7.3762;MLEAC=4;MLEAF=1.00;MQ=56.04;MQ0=0;QD=32.38;VQSLOD=2.27;culprit=HaplotypeScore        GT:AD:DP:GQ:PL  1/1:0,998:998:99:32010,2926,0   1/1:0,999:999:99:32767,2912,0
chrM    711     .       G       A       62989.20        PASS    AC=4;AF=1.00;AN=4;BaseQRankSum=2.500;DP=2000;Dels=0.00;FS=3.751;HaplotypeScore=8.7084;MLEAC=4;MLEAF=1.00;MQ=56.74;MQ0=1;MQRankSum=-0.107;QD=31.49;ReadPosRankSum=-2.169;VQSLOD=2.46;culprit=HaplotypeScore
      GT:AD:DP:GQ:PL  1/1:0,998:972:99:30899,2808,0   1/1:3,997:972:99:32117,2830,0
chrM    1121    .       T       C       16719.20        Nov28filters && QD < 2.0 && ReadPosRankSum < -8.0 && MQ < 40.0 && FS > 60.0 && MQRandkSum < -12.5;VQSRTrancheSNP99.90to100.00   AC=4;AF=1.00;AN=4;BaseQRankSum=-0.239;DP=2000;Dels=0.00;FS=2.141;HaplotypeScore=22.9003;MLEAC=4;MLEAF=1.00;MQ=21.32;MQ0=703;MQRankSum=-1.627;QD=8.36;ReadPosRankSum=-0.027;VQSLOD=-4.195e+00;culprit=HaplotypeScore     GT:AD:DP:GQ:PL  1/1:3,985:986:99:9547,976,0     1/1:4,983:983:99:7199,739,0
chrM    2489    .       A       C       34.19   LowQual;Nov28filters && QD < 2.0 && ReadPosRankSum < -8.0 && MQ < 40.0 && FS > 60.0 && MQRandkSum < -12.5       AC=1;AF=0.250;AN=4;BaseQRankSum=-17.321;DP=2000;Dels=0.00;FS=180.208;HaplotypeScore=18.7245;MLEAC=1;MLEAF=0.250;MQ=46.52;MQ0=31;MQRankSum=3.365;QD=0.03;ReadPosRankSum=-4.198   GT:AD:DP:GQ:PL  0/1:278,719:950:64:64,0,4623    0/0:309,688:950:99:0,263,6065

For the filter option, most of the filtered snps show Nov28filters rather than PASS or LowQual, what's wrong with that, Are there some problems with my command lines? Thank you so much for your reply.

Comments (1)

HI

I am using the following set of commands on GATK2.1.13 to generate a VCF file

echo `java -Xmx20g -jar /usr/bin/GenomeAnalysisTK.jar -I B2_with_ReadGroup.ddup.sorted.bam -R human_g1k_v37.fasta -T RealignerTargetCreator  -o my.intervals -et NO_ET -K /root/sandbox/saket.kumar_iitb.ac.in.key`
echo "Realignment Done at `date`"
echo "Starting IndelRealigner at `date`"

echo `java -Xmx20g -jar /usr/bin/GenomeAnalysisTK.jar -I B2_with_ReadGroup.ddup.sorted.bam -R human_g1k_v37.fasta -T IndelRealigner -targetIntervals my.intervals -o myrealignedBam.bam  -et NO_ET -K /root/sandbox/saket.kumar_iitb.ac.in.key`
echo "Realignment done at `date`"
echo "Starting UnifiedGenotyper at `date`"
echo `java -Xmx20g -jar /usr/bin/GenomeAnalysisTK.jar -l INFO -R human_g1k_v37.fasta -T UnifiedGenotyper    -I myrealignedBam.bam    -o mygatk_vcf.vcf    --output_mode EMIT_ALL_SITES -et NO_ET -K /root/sandbox/saket.kumar_iitb.ac.in.key`
echo "Gentoypxing complete at `date`"

When i do a 'mpileup' for B2_with_ReadGroup.ddup.sorted.bam , I get a devcent 10 MB VCF file. But on the last ste of the above pipeline, my " mygatk_vcf.vcf " is goinging into 81GBs !!

Do you know what is wrong ?

Comments (2)

Hi,

Could you tell me when we can use new version of SnpEff with GATK?

I have some bugs :

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-35-g2d70733):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Could not create module ActiveRegionBasedAnnotation because BUG: Cannot find expected constructor for class caused by exception org.broadinstitute.sting.gatk.walkers

.annotator.interfaces.ActiveRegionBasedAnnotation.()

ERROR ------------------------------------------------------------------------------------------
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-35-g2d70733):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Could not create module ExperimentalAnnotation because BUG: Cannot find expected constructor for class

caused by exception org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation.()

ERROR ------------------------------------------------------------------------------------------
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.0-35-g2d70733):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Could not create module RankSumTest because BUG: cannot instantiate class: must be concrete class caused by exception null
ERROR ------------------------------------------------------------------------------------------

I don't know if I forget some other options linked these annotations. These options are important for me. So I deleted them but if somebody want to use them ...

Regards,

Tiphaine