1000Genomes vcf file and correct reference genome used in FastaAlternateReferenceMaker giving error

I am using a vcf file from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Specifically, chromosome 20.

1000Genomes says their reference genome is GRCh37, which is the same as hg19. However, when I attempt to use

java -jar GenomeAnalysisTK.jar \
   -T FastaAlternateReferenceMaker \
   -R chr20.fa \
   -o phase3_human_chr20.fa \
   -V ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf 

I get this error:

ERROR MESSAGE: Input files /san/data/GATK/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf and reference have incompatible contigs. Please see https://www.broadinstitute.org/gatk/guide/article?id=63for more information. Error details: No overlapping contigs found

I've read through https://software.broadinstitute.org/gatk/guide/article?id=63 and have tried to fix the error myself. However, the reference genome for the vcf file was hg19, and I cannot see any other genome I can use. Could there possibly be another error I am not seeing?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @tostitos
    Hi,

    Can you please post your FASTA .dict file and VCF header here?

    Thanks,
    Sheila

  • rajeshkemauryarajeshkemaurya BengaloreMember

    Hello ma'am I am getting same problem here with my experiment....

    as You mentioned ,
    I am attaching the .dict and vcf header here.

    fileformat=VCFv4.2

    ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">

    FILTER=<ID=InbreedingCoeff_Filter,Description="InbreedingCoeff <= -0.8">

    FILTER=<ID=LowQual,Description="Low quality">

    FILTER=<ID=NewCut_Filter,Description="VQSLOD > -2.632 && InbreedingCoeff >-0.8">

    FILTER=<ID=VQSRTrancheINDEL95.00to96.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: 0.9503 <= x < 1.2168">

    FILTER=<ID=VQSRTrancheINDEL96.00to97.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: 0.7622 <= x < 0.9503">

    FILTER=<ID=VQSRTrancheINDEL97.00to99.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: 0.0426 <= x < 0.7622">

    FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -0.8363 <= x < 0.0426">

    FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -8.5421 <= x < -0.8363">

    FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -18.4482 <= x < -8.5421">

    FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -37254.4742">

    FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -37254.4742 <= x < -18.4482">

    FILTER=<ID=VQSRTrancheSNP99.60to99.80,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -4.9627 <= x < -1.8251">

    FILTER=<ID=VQSRTrancheSNP99.80to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -31.4709 <= x < -4.9627">

    FILTER=<ID=VQSRTrancheSNP99.90to99.95,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -170.3725 <= x < -31.4709">

    FILTER=<ID=VQSRTrancheSNP99.95to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39645.8352">

    FILTER=<ID=VQSRTrancheSNP99.95to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -39645.8352 <= x < -170.3725">

    FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

    FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

    FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

    FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

    FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">

    FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

    FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">

    GATKCommandLine=<ID=ApplyRecalibration,Version=3.1-163-g4284d7a,Date="Fri Jun 06 05:42:47 EDT 2014",Epoch=1402047767783,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/seq/dax/macarthur_joint_calling/v2/scattered/temp_0001_of_1000/scattered.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=true num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/seq/dax/macarthur_joint_calling/v2/scattered/temp_0001_of_1000/genotypes.unfiltered.vcf.gz)] recal_file=(RodBinding name=recal_file source=/seq/dax/macarthur_joint_calling/v2/macarthur_joint_calling.indels.recal) tranches_file=/seq/dax/macarthur_joint_calling/v2/macarthur_joint_calling.indels.tranches out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub ts_filter_level=95.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GATKCommandLine=<ID=SelectVariants,Version=3.3-33-g58cfab1,Date="Fri Nov 21 21:05:54 EST 2014",Epoch=1416621954228,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/humgen/gsa-firehose/ExAC_GATKV2.5/MacArthur_HC/v2/fullset/ExAC_HC.chrX.00.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=[exac_panel.samples] exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=true excludeFiltered=false preserveAlleles=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GATKCommandLine=<ID=VariantAnnotator,Version=3.2-2-gec30cee,Date="Mon Nov 24 21:39:16 EST 2014",Epoch=1416883156611,CommandLineOptions="analysis_type=VariantAnnotator input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[X:1-7763528] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=../filtered/ExAC_HC.chrX.00.filtered.vcf.gz) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name= source=UNBOUND) comp=[] resource=[] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub annotation=[SexAlleleCounts] excludeAnnotation=[] group=[] expression={} useAllAnnotations=false list=false alwaysAppendDbsnpId=false MendelViolationGenotypeQualityThreshold=0.0 sampleMappingFile=samples_pop_sex.tsv filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GATKCommandLine=<ID=VariantFiltration,Version=3.2-2-gec30cee,Date="Sun Nov 23 08:50:16 EST 2014",Epoch=1416750616237,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[X:1-7763528] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=../fullset/ExAC_HC.chrX.00.vcf.gz) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub filterExpression=[VQSLOD > -2.632 && InbreedingCoeff >-0.8, InbreedingCoeff <= -0.8] filterName=[NewCut_Filter, InbreedingCoeff_Filter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive)

    INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

    INFO=<ID=AC_AFR,Number=A,Type=Integer,Description="African/African American Allele Counts">

    INFO=<ID=AC_AMR,Number=A,Type=Integer,Description="American Allele Counts">

    INFO=<ID=AC_Adj,Number=A,Type=Integer,Description="Adjusted Allele Counts">

    INFO=<ID=AC_EAS,Number=A,Type=Integer,Description="East Asian Allele Counts">

    INFO=<ID=AC_FIN,Number=A,Type=Integer,Description="Finnish Allele Counts">

    INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description="Adjusted Hemizygous Counts">

    INFO=<ID=AC_Het,Number=A,Type=Integer,Description="Adjusted Heterozygous Counts">

    INFO=<ID=AC_Hom,Number=A,Type=Integer,Description="Adjusted Homozygous Counts">

    INFO=<ID=AC_NFE,Number=A,Type=Integer,Description="Non-Finnish European Allele Counts">

    INFO=<ID=AC_OTH,Number=A,Type=Integer,Description="Other Allele Counts">

    INFO=<ID=AC_SAS,Number=A,Type=Integer,Description="South Asian Allele Counts">

    INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

    INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">

    INFO=<ID=AN_AFR,Number=1,Type=Integer,Description="African/African American Chromosome Count">

    INFO=<ID=AN_AMR,Number=1,Type=Integer,Description="American Chromosome Count">

    INFO=<ID=AN_Adj,Number=1,Type=Integer,Description="Adjusted Chromosome Count">

    INFO=<ID=AN_EAS,Number=1,Type=Integer,Description="East Asian Chromosome Count">

    INFO=<ID=AN_FIN,Number=1,Type=Integer,Description="Finnish Chromosome Count">

    INFO=<ID=AN_NFE,Number=1,Type=Integer,Description="Non-Finnish European Chromosome Count">

    INFO=<ID=AN_OTH,Number=1,Type=Integer,Description="Other Chromosome Count">

    INFO=<ID=AN_SAS,Number=1,Type=Integer,Description="South Asian Chromosome Count">

    INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

    INFO=<ID=CCC,Number=1,Type=Integer,Description="Number of called chromosomes">

    INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">

    INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">

    INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

    INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">

    INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">

    INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">

    INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values">

    INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values">

    INFO=<ID=HWP,Number=1,Type=Float,Description="P value from test of Hardy Weinberg Equilibrium">

    INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">

    INFO=<ID=Hemi_AFR,Number=A,Type=Integer,Description="African/African American Hemizygous Counts">

    INFO=<ID=Hemi_AMR,Number=A,Type=Integer,Description="American Hemizygous Counts">

    INFO=<ID=Hemi_EAS,Number=A,Type=Integer,Description="East Asian Hemizygous Counts">

    INFO=<ID=Hemi_FIN,Number=A,Type=Integer,Description="Finnish Hemizygous Counts">

    INFO=<ID=Hemi_NFE,Number=A,Type=Integer,Description="Non-Finnish European Hemizygous Counts">

    INFO=<ID=Hemi_OTH,Number=A,Type=Integer,Description="Other Hemizygous Counts">

    INFO=<ID=Hemi_SAS,Number=A,Type=Integer,Description="South Asian Hemizygous Counts">

    INFO=<ID=Het_AFR,Number=.,Type=Integer,Description="African/African American Heterozygous Counts">

    INFO=<ID=Het_AMR,Number=.,Type=Integer,Description="American Heterozygous Counts">

    INFO=<ID=Het_EAS,Number=.,Type=Integer,Description="East Asian Heterozygous Counts">

    INFO=<ID=Het_FIN,Number=.,Type=Integer,Description="Finnish Heterozygous Counts">

    INFO=<ID=Het_NFE,Number=.,Type=Integer,Description="Non-Finnish European Heterozygous Counts">

    INFO=<ID=Het_OTH,Number=.,Type=Integer,Description="Other Heterozygous Counts">

    INFO=<ID=Het_SAS,Number=.,Type=Integer,Description="South Asian Heterozygous Counts">

    INFO=<ID=Hom_AFR,Number=A,Type=Integer,Description="African/African American Homozygous Counts">

    INFO=<ID=Hom_AMR,Number=A,Type=Integer,Description="American Homozygous Counts">

    INFO=<ID=Hom_EAS,Number=A,Type=Integer,Description="East Asian Homozygous Counts">

    INFO=<ID=Hom_FIN,Number=A,Type=Integer,Description="Finnish Homozygous Counts">

    INFO=<ID=Hom_NFE,Number=A,Type=Integer,Description="Non-Finnish European Homozygous Counts">

    INFO=<ID=Hom_OTH,Number=A,Type=Integer,Description="Other Homozygous Counts">

    INFO=<ID=Hom_SAS,Number=A,Type=Integer,Description="South Asian Homozygous Counts">

    INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">

    INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

    INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

    INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">

    INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">

    INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">

    INFO=<ID=NCC,Number=1,Type=Integer,Description="Number of no-called samples">

    INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">

    INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">

    INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">

    INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">

    INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">

    INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">

    contig=<ID=1,length=249250621>

    contig=<ID=2,length=243199373>

    contig=<ID=3,length=198022430>

    contig=<ID=4,length=191154276>

    contig=<ID=5,length=180915260>

    contig=<ID=6,length=171115067>

    contig=<ID=7,length=159138663>

    contig=<ID=8,length=146364022>

    contig=<ID=9,length=141213431>

    contig=<ID=10,length=135534747>

    contig=<ID=11,length=135006516>

    contig=<ID=12,length=133851895>

    contig=<ID=13,length=115169878>

    contig=<ID=14,length=107349540>

    contig=<ID=15,length=102531392>

    contig=<ID=16,length=90354753>

    contig=<ID=17,length=81195210>

    contig=<ID=18,length=78077248>

    contig=<ID=19,length=59128983>

    contig=<ID=20,length=63025520>

    contig=<ID=21,length=48129895>

    contig=<ID=22,length=51304566>

    contig=<ID=X,length=155270560>

    contig=<ID=Y,length=59373566>

    contig=<ID=MT,length=16569>

    contig=<ID=GL000207.1,length=4262>

    contig=<ID=GL000226.1,length=15008>

    contig=<ID=GL000229.1,length=19913>

    contig=<ID=GL000231.1,length=27386>

    contig=<ID=GL000210.1,length=27682>

    contig=<ID=GL000239.1,length=33824>

    contig=<ID=GL000235.1,length=34474>

    contig=<ID=GL000201.1,length=36148>

    contig=<ID=GL000247.1,length=36422>

    contig=<ID=GL000245.1,length=36651>

    contig=<ID=GL000197.1,length=37175>

    contig=<ID=GL000203.1,length=37498>

    contig=<ID=GL000246.1,length=38154>

    contig=<ID=GL000249.1,length=38502>

    contig=<ID=GL000196.1,length=38914>

    contig=<ID=GL000248.1,length=39786>

    contig=<ID=GL000244.1,length=39929>

    contig=<ID=GL000238.1,length=39939>

    contig=<ID=GL000202.1,length=40103>

    contig=<ID=GL000234.1,length=40531>

    contig=<ID=GL000232.1,length=40652>

    contig=<ID=GL000206.1,length=41001>

    contig=<ID=GL000240.1,length=41933>

    contig=<ID=GL000236.1,length=41934>

    contig=<ID=GL000241.1,length=42152>

    contig=<ID=GL000243.1,length=43341>

    contig=<ID=GL000242.1,length=43523>

    contig=<ID=GL000230.1,length=43691>

    contig=<ID=GL000237.1,length=45867>

    contig=<ID=GL000233.1,length=45941>

    contig=<ID=GL000204.1,length=81310>

    contig=<ID=GL000198.1,length=90085>

    contig=<ID=GL000208.1,length=92689>

    contig=<ID=GL000191.1,length=106433>

    contig=<ID=GL000227.1,length=128374>

    contig=<ID=GL000228.1,length=129120>

    contig=<ID=GL000214.1,length=137718>

    contig=<ID=GL000221.1,length=155397>

    contig=<ID=GL000209.1,length=159169>

    contig=<ID=GL000218.1,length=161147>

    contig=<ID=GL000220.1,length=161802>

    contig=<ID=GL000213.1,length=164239>

    contig=<ID=GL000211.1,length=166566>

    contig=<ID=GL000199.1,length=169874>

    contig=<ID=GL000217.1,length=172149>

    contig=<ID=GL000216.1,length=172294>

    contig=<ID=GL000215.1,length=172545>

    contig=<ID=GL000205.1,length=174588>

    contig=<ID=GL000219.1,length=179198>

    contig=<ID=GL000224.1,length=179693>

    contig=<ID=GL000223.1,length=180455>

    contig=<ID=GL000195.1,length=182896>

    contig=<ID=GL000212.1,length=186858>

    contig=<ID=GL000222.1,length=186861>

    contig=<ID=GL000200.1,length=187035>

    contig=<ID=GL000193.1,length=189789>

    contig=<ID=GL000194.1,length=191469>

    contig=<ID=GL000225.1,length=211173>

    contig=<ID=GL000192.1,length=547496>

    contig=<ID=NC_007605,length=171823>

    reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta

    source=SelectVariants

    INFO=<ID=DP_HIST,Number=R,Type=String,Description="Histogram for DP; Mids: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">

    INFO=<ID=GQ_HIST,Number=R,Type=String,Description="Histogram for GQ; Mids: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5">

    INFO=<ID=DOUBLETON_DIST,Number=A,Type=String,Description="Euclidean distance of carriers of doubletons">

    INFO=<ID=AC_MALE,Number=A,Type=String,Description="Allele count among males">

    INFO=<ID=AC_FEMALE,Number=A,Type=String,Description="Allele count among females">

    INFO=<ID=AN_MALE,Number=1,Type=String,Description="Allele number among males">

    INFO=<ID=AN_FEMALE,Number=1,Type=String,Description="Allele number among females">

    INFO=<ID=AC_CONSANGUINEOUS,Number=A,Type=String,Description="Allele count among individuals with F > 0.05">

    INFO=<ID=AN_CONSANGUINEOUS,Number=1,Type=String,Description="Allele number among individuals with F > 0.05">

    INFO=<ID=Hom_CONSANGUINEOUS,Number=A,Type=String,Description="Homozygote count among individuals with F > 0.05">

    VEP=v81 cache=/humgen/atgu1/fs03/konradk/vep//homo_sapiens/81_GRCh37 db=. polyphen=2.2.2 sift=sift5.2.2 COSMIC=71 ESP=20141103 gencode=GENCODE 19 HGMD-PUBLIC=20144 genebuild=2011-04 regbuild=13 assembly=GRCh37.p13 dbSNP=142 ClinVar=201501

    LoF_info=Info used for LoF annotation

    LoF_flags=Possible warning flags for LoF

    LoF_filter=Reason for LoF not being HC

    LoF=Loss-of-function annotation (HC = High Confidence; LC = Low Confidence)

    context=1 base context around the variant

    ancestral=ancestral allele

    INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|VARIANT_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|GMAF|AFR_MAF|AMR_MAF|ASN_MAF|EAS_MAF|EUR_MAF|SAS_MAF|AA_MAF|EA_MAF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|LoF_info|LoF_flags|LoF_filter|LoF|context|ancestral">

    INFO=<ID=AC_POPMAX,Number=A,Type=String,Description="AC in the population with the max AF">

    INFO=<ID=AN_POPMAX,Number=A,Type=String,Description="AN in the population with the max AF">

    INFO=<ID=POPMAX,Number=A,Type=String,Description="Population with max AF">

    INFO=<ID=clinvar_measureset_id,Number=A,Type=String,Description="Clinvar Measureset ID">

    INFO=<ID=clinvar_conflicted,Number=A,Type=String,Description="Clinvar Conflicted Status">

    INFO=<ID=clinvar_pathogenic,Number=A,Type=String,Description="Clinvar Pathogenic Status">

    INFO=<ID=clinvar_mut,Number=A,Type=String,Description="Clinvar MUT Flag (is disease allele REF?)">

    INFO=<ID=K1_RUN,Number=A,Type=String,Description="Number of ensuing single nucleotide repeats.">

    INFO=<ID=K2_RUN,Number=A,Type=String,Description="Number of ensuing di-nucleotide repeats.">

    INFO=<ID=K3_RUN,Number=A,Type=String,Description="Number of ensuing tri-nucleotide repeats.">

    INFO=<ID=ESP_AF_POPMAX,Number=A,Type=String,Description="Max allele frequency across populations in ESP">

    INFO=<ID=ESP_AF_GLOBAL,Number=A,Type=String,Description="Overall allele frequency in ESP">

    INFO=<ID=ESP_AC,Number=A,Type=String,Description="Allele Count in ESP">

    INFO=<ID=KG_AF_POPMAX,Number=A,Type=String,Description="Max allele frequency across populations in 1000 Genomes">

    INFO=<ID=KG_AF_GLOBAL,Number=A,Type=String,Description="Overall allele frequency in 1000 Genomes">

    INFO=<ID=KG_AC,Number=A,Type=String,Description="Allele Count in 1000 Genomes">

    CHROM POS ID REF ALT QUAL FILTER INFO

    1 13372 . G C 608.91 PASS AC=3;AC_AFR=0;AC_AMR=0;AC_Adj=2;AC_EAS=0;AC_FIN=0;AC_Het=0;AC_Hom=1;AC_NFE=0;AC_OTH=0;AC_SAS=2;AF=6.998e-05;AN=42870;AN_AFR=770;AN_AMR=134;AN_Adj=8432;AN_EAS=254;AN_FIN=16;AN_NFE=2116;AN_OTH=90;AN_SAS=5052;BaseQRankSum=0.727;ClippingRankSum=1.15;DP=139843;FS=0.000;GQ_MEAN=12.48;GQ_STDDEV=15.18;Het_AFR=0;Het_AMR=0;Het_EAS=0;Het_FIN=0;Het_NFE=0;Het_OTH=0;Het_SAS=0;Hom_AFR=0;Hom_AMR=0;Hom_EAS=0;Hom_FIN=0;Hom_NFE=0;Hom_OTH=0;Hom_SAS=1;InbreedingCoeff=-0.0844;MQ=35.72;MQ0=0;MQRankSum=0.727;NCC=60853;QD=23.42;ReadPosRankSum=0.727;VQSLOD=-1.687e+00;culprit=MQ;DP_HIST=14728|2455|2120|518|121|499|534|314|111|21|10|2|2|0|0|0|0|0|0|0,1|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0;GQ_HIST=1012|14971|172|100|3161|259|127|30|8|9|5|16|1162|274|59|45|17|2|3|3,0|0|0|0|0|1|0|0|0|0|0|0|0|1|0|0|0|0|0

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @rajeshkemaurya
    Hi,

    The issue is that the contigs in your reference and VCF do not match. Notice the reference has chr at the beginning of the contig number. You need to make sure the reference is the exact same reference you aligned your reads to and called variants on.

    -Sheila

  • rajeshkemauryarajeshkemaurya BengaloreMember

    Thanks!
    but now the problem came is that
    "Output file has differ in length of reference file"

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @rajeshkemaurya
    Hi,

    Okay, can you please post the exact command you ran? Please also post the complete log output and error message.

    Thanks,
    Sheila

  • rajeshkemauryarajeshkemaurya BengaloreMember

    Hi,

    Let me explain you my whole process what i performed. It will be good to you to understand my problem.

    I extracted chr21.vcf file from ExAC.r0.3.1.sites.vep.vcf.gz by using command given below:
    tabix -h ExAC.r0.3.1.sites.vep.vcf.gz 21 > chr21.vcf
    then i did bgzip and tabix operation
    bgzip -c chr21.vcf > chr21.vcf.gz
    tabix -p vcf chr21.vcf.gz----it gives output chr21.vcf.gz.tbi

    Then i proceeded towards the GATK

    • Generated the BWA indexed file
      bwa index -a bwtsw chr21.fa

    • Generated fasta file index from samtool (we can download it from ftp link given above with reference genome)
      samtools faidx chr21.fa

    • Generate Sequence Directory from picard tool (we can download it from ftp link given above with reference genome)
      java -jar picard.jar CreateSequenceDictionary \R=chr21.fasta \O=chr21.dict

    • Now run the GATK command for the FastaAlternateReferenceMaker
      java -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R chr21.fa -o altref.fa -V ExAC.r1.sites.vep.vcf.gz -L chr21

    but it showing warning:
    Done. There were 1 WARN messages, the first 1 are repeated below.
    WARN 10:58:29,423 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation

    IT HAS GIVEN SAME LENGTH AS OF REFERENCE IN OUTPUT BUT WITH SAME FILE WITH NO DIFFERENCE....
    Please find the snapshot given below: pic1

    Then i have gone through the one page of link (http://plindenbaum.blogspot.in/2011/10/reference-genome-with-or-without-chr.html)
    So i followed the same what they instructed here by using command given below:

    sed 's/^chr//' chr21.fa.fai > chr21_NOPREFIX.fa.fai

    ln -s chr21.fa chr21_NOPREFIX.fa

    java -jar picard.jar CreateSequenceDictionary \R=chr21_NOPREFIX.fa \O=chr21.dict (i performed this because it was showing the .dict file missing)

    java -jar GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R chr21_NOPREFIX.fa -o altref.fa -V chr21.vcf.gz -L 21

    IT HAS GIVEN different LENGTH AS OF REFERENCE ....
    Please find the snapshot given below: pic2

    I also have one doubt: is it mandatory that output file and reference file should have to be same length.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @rajeshkemaurya
    Hi,

    I think this is an issue with the gzipped files. Have a look at this thread.

    -Sheila

  • rajeshkemauryarajeshkemaurya BengaloreMember

    Thanks!
    I solved the gzipped problem. No i did not get any error.

    But problem is the the output file differ in length of reference file.

    refchr20

    63025520

    1 20:1

    63018005

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @rajeshkemaurya
    Hi,

    I think I see what you are asking! You want to know why the output reference has a different length than the input reference? If so, that is nothing to worry about. Sometimes there are insertions or deletions that are added to the output reference from the input VCF that changes the length. For example, let's say you have a deletion in the VCF at positions 2 and 3, then:

    OLD_REF: ATGC
    becomes:
    NEW_REF: AC

    I hope that helps.

    -Sheila

Sign In or Register to comment.