We support the Variant Call Format (VCF) for variant callsets. No other file formats are supported.
VCFTools contains a validation tool that will allow you to verify it.
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.
Hi,
Could you tell me when we can use new version of SnpEff with GATK?
I have some bugs :
.annotator.interfaces.ActiveRegionBasedAnnotation.
caused by exception org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation.
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
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 ?
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.