Question: ERROR MESSAGE: Your input file has a malformed header: VCFv4.2 is not a supported version - Eval Variant Tool
0
gravatar for bio_vitus
2.5 years ago by
bio_vitus0
United States
bio_vitus0 wrote:
Hi,

I am getting this error when running eval variant tool from GATK ver 2.8 in galaxy.


ERROR MESSAGE: Your input file has a malformed header: VCFv4.2 is not a supported version

 

I am enclosing the header of vcf file which I am using to run eval variant tool and like to know if anybody can help.

Appreciate and thank you.

##fileformat=VCFv4.1
##fileDate=20151027
##source=freeBayes v0.9.18
##reference=/mnt/galaxyIndices/genomes/hg38/sam_indexes/hg38/hg38.fa
##phasing=none
##commandline="freebayes --bam localbam_0.bam --fasta-reference /mnt/galaxyIndices/genomes/hg38/sam_indexes/hg38/hg38.fa --vcf /mnt/galaxy/files/000/dataset_791.dat"
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">

 

vcf gatk • 2.8k views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson24k • written 2.5 years ago by bio_vitus0
0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Are there other VCF inputs to the tool that are in version 4.2?

I should note that GATK 2 was undergoing changes to handle the different flavors of VCF files at one point. Whether all of these changes made it into the binary in use by the Galaxy wrapped version if not clear. You could content the repository owners (IUC) through the Tool Shed after confirming inputs and still having problems.

These same tool authors are considering upgrading to GATK to v3. Progress can be followed here: https://github.com/galaxyproject/tools-iuc/issues/194

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson24k

Dear Ms. Jen,

Thank you for your reply. There are two other VCF inputs to the tool. Actually, I am using Mpileup, Freebayes and GATK unified genotyper in galaxy.

The Mpileup generates VCF file in version 4.2 format and freebayes, GATK unified genotyper generates VCF file in version 4.1 format in galaxy. Looks like that is causing the problem and I am enclosing the headers of VCF output from Mpileup and GATK unified genotyper.

Is it possible to fix VCF output from Freebayes and GATK unified genotyper so that they are all in one VCF file format.

Appreciate your help and thank you.

bio_vitus

 

VCF file header 1

##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##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=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.8-1-g932cd3a,Date="Wed Oct 28 20:09:24 UTC 2015",Epoch=1446062964313,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/mnt/galaxy/tmp/tmp-gatk-3cMEoy/gatk_input_0.bam] 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=/mnt/galaxyIndices/genomes/hg38/gatk_picard_index/hg38/hg38.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=STRICT 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 genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name=dbsnp source=/mnt/galaxy/tmp/tmp-gatk-3cMEoy/input_dbsnp_dbsnp.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##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=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##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=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##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=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##contig=<ID=chrM,length=16569>
##contig=<ID=chr11_KI270721v1_random,length=100316>
##contig=<ID=chr14_GL000009v2_random,length=201709>
##contig=<ID=chr14_GL000225v1_random,length=211173>
##contig=<ID=chr14_KI270722v1_random,length=194050>
##contig=<ID=chr14_GL000194v1_random,length=191469>
##contig=<ID=chr14_KI270723v1_random,length=38115>
##contig=<ID=chr14_KI270724v1_random,length=39555>
##contig=<ID=chr14_KI270725v1_random,length=172810>
##contig=<ID=chr14_KI270726v1_random,length=43739>
##contig=<ID=chr15_KI270727v1_random,length=448248>
##contig=<ID=chr16_KI270728v1_random,length=1872759>
##contig=<ID=chr17_GL000205v2_random,length=185591>
##contig=<ID=chr17_KI270729v1_random,length=280839>
##contig=<ID=chr17_KI270730v1_random,length=112551>
##contig=<ID=chr1_KI270706v1_random,length=175055>
##contig=<ID=chr1_KI270707v1_random,length=32032>
##contig=<ID=chr1_KI270708v1_random,length=127682>
##contig=<ID=chr1_KI270709v1_random,length=66860>
##contig=<ID=chr1_KI270710v1_random,length=40176>
##contig=<ID=chr1_KI270711v1_random,length=42210>
##contig=<ID=chr1_KI270712v1_random,length=176043>
##contig=<ID=chr1_KI270713v1_random,length=40745>
##contig=<ID=chr1_KI270714v1_random,length=41717>
##contig=<ID=chr22_KI270731v1_random,length=150754>
##contig=<ID=chr22_KI270732v1_random,length=41543>
##contig=<ID=chr22_KI270733v1_random,length=179772>
##contig=<ID=chr22_KI270734v1_random,length=165050>
##contig=<ID=chr22_KI270735v1_random,length=42811>
##contig=<ID=chr22_KI270736v1_random,length=181920>
##contig=<ID=chr22_KI270737v1_random,length=103838>
##contig=<ID=chr22_KI270738v1_random,length=99375>
##contig=<ID=chr22_KI270739v1_random,length=73985>
##contig=<ID=chr2_KI270715v1_random,length=161471>
##contig=<ID=chr2_KI270716v1_random,length=153799>
##contig=<ID=chr3_GL000221v1_random,length=155397>
##contig=<ID=chr4_GL000008v2_random,length=209709>
##contig=<ID=chr5_GL000208v1_random,length=92689>
##contig=<ID=chr9_KI270717v1_random,length=40062>
##contig=<ID=chr9_KI270718v1_random,length=38054>
##contig=<ID=chr9_KI270719v1_random,length=176845>
##contig=<ID=chr9_KI270720v1_random,length=39050>
##contig=<ID=chr1_KI270762v1_alt,length=354444>
##contig=<ID=chr1_KI270766v1_alt,length=256271>
##contig=<ID=chr1_KI270760v1_alt,length=109528>
##contig=<ID=chr1_KI270765v1_alt,length=185285>
##contig=<ID=chr1_GL383518v1_alt,length=182439>
##contig=<ID=chr1_GL383519v1_alt,length=110268>
##contig=<ID=chr1_GL383520v2_alt,length=366580>
##contig=<ID=chr1_KI270764v1_alt,length=50258>
##contig=<ID=chr1_KI270763v1_alt,length=911658>
##contig=<ID=chr1_KI270759v1_alt,length=425601>
##contig=<ID=chr1_KI270761v1_alt,length=165834>
##contig=<ID=chr2_KI270770v1_alt,length=136240>
##contig=<ID=chr2_KI270773v1_alt,length=70887>
##contig=<ID=chr2_KI270774v1_alt,length=223625>
##contig=<ID=chr2_KI270769v1_alt,length=120616>
##contig=<ID=chr2_GL383521v1_alt,length=143390>
##contig=<ID=chr2_KI270772v1_alt,length=133041>
##contig=<ID=chr2_KI270775v1_alt,length=138019>
##contig=<ID=chr2_KI270771v1_alt,length=110395>
##contig=<ID=chr2_KI270768v1_alt,length=110099>
##contig=<ID=chr2_GL582966v2_alt,length=96131>
##contig=<ID=chr2_GL383522v1_alt,length=123821>
##contig=<ID=chr2_KI270776v1_alt,length=174166>
##contig=<ID=chr2_KI270767v1_alt,length=161578>
##contig=<ID=chr3_JH636055v2_alt,length=173151>
##contig=<ID=chr3_KI270783v1_alt,length=109187>
##contig=<ID=chr3_KI270780v1_alt,length=224108>
##contig=<ID=chr3_GL383526v1_alt,length=180671>
##contig=<ID=chr3_KI270777v1_alt,length=173649>
##contig=<ID=chr3_KI270778v1_alt,length=248252>
##contig=<ID=chr3_KI270781v1_alt,length=113034>
##contig=<ID=chr3_KI270779v1_alt,length=205312>
##contig=<ID=chr3_KI270782v1_alt,length=162429>
##contig=<ID=chr3_KI270784v1_alt,length=184404>
##contig=<ID=chr4_KI270790v1_alt,length=220246>
##contig=<ID=chr4_GL383528v1_alt,length=376187>
##contig=<ID=chr4_KI270787v1_alt,length=111943>
##contig=<ID=chr4_GL000257v2_alt,length=586476>
##contig=<ID=chr4_KI270788v1_alt,length=158965>
##contig=<ID=chr4_GL383527v1_alt,length=164536>
##contig=<ID=chr4_KI270785v1_alt,length=119912>
##contig=<ID=chr4_KI270789v1_alt,length=205944>
##contig=<ID=chr4_KI270786v1_alt,length=244096>
##contig=<ID=chr5_KI270793v1_alt,length=126136>
##contig=<ID=chr5_KI270792v1_alt,length=179043>
##contig=<ID=chr5_KI270791v1_alt,length=195710>
##contig=<ID=chr5_GL383532v1_alt,length=82728>
##contig=<ID=chr5_GL949742v1_alt,length=226852>
##contig=<ID=chr5_KI270794v1_alt,length=164558>
##contig=<ID=chr5_GL339449v2_alt,length=1612928>
##contig=<ID=chr5_GL383530v1_alt,length=101241>
##contig=<ID=chr5_KI270796v1_alt,length=172708>
##contig=<ID=chr5_GL383531v1_alt,length=173459>
##contig=<ID=chr5_KI270795v1_alt,length=131892>
##contig=<ID=chr6_GL000250v2_alt,length=4672374>
##contig=<ID=chr6_KI270800v1_alt,length=175808>
##contig=<ID=chr6_KI270799v1_alt,length=152148>
##contig=<ID=chr6_GL383533v1_alt,length=124736>
##contig=<ID=chr6_KI270801v1_alt,length=870480>
##contig=<ID=chr6_KI270802v1_alt,length=75005>
##contig=<ID=chr6_KB021644v2_alt,length=185823>
##contig=<ID=chr6_KI270797v1_alt,length=197536>
##contig=<ID=chr6_KI270798v1_alt,length=271782>
##contig=<ID=chr7_KI270804v1_alt,length=157952>
##contig=<ID=chr7_KI270809v1_alt,length=209586>
##contig=<ID=chr7_KI270806v1_alt,length=158166>
##contig=<ID=chr7_GL383534v2_alt,length=119183>
##contig=<ID=chr7_KI270803v1_alt,length=1111570>
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VCF file header 2

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.2+htslib-1.2.1
##samtoolsCommand=samtools mpileup -f /mnt/galaxyIndices/genomes/hg38/sam_indexes/hg38/hg38.fa -l /mnt/galaxy/files/000/dataset_603.dat -C 0 -d 250 -q 0 -Q 13 --VCF --uncompressed --output /mnt/galaxy/files/000/dataset_622.dat /mnt/galaxy/files/000/dataset_608.dat
##reference=file:///mnt/galaxyIndices/genomes/hg38/sam_indexes/hg38/hg38.fa
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##contig=<ID=chrM,length=16571>
##contig=<ID=chr11_gl000202_random,length=40103>
##contig=<ID=chr17_ctg5_hap1,length=1680828>
##contig=<ID=chr17_gl000203_random,length=37498>
##contig=<ID=chr17_gl000204_random,length=81310>
##contig=<ID=chr17_gl000205_random,length=174588>
##contig=<ID=chr17_gl000206_random,length=41001>
##contig=<ID=chr18_gl000207_random,length=4262>
##contig=<ID=chr19_gl000208_random,length=92689>
##contig=<ID=chr19_gl000209_random,length=159169>
##contig=<ID=chr1_gl000191_random,length=106433>
##contig=<ID=chr1_gl000192_random,length=547496>
##contig=<ID=chr21_gl000210_random,length=27682>
##contig=<ID=chr4_ctg9_hap1,length=590426>
##contig=<ID=chr4_gl000193_random,length=189789>
##contig=<ID=chr4_gl000194_random,length=191469>
##contig=<ID=chr6_apd_hap1,length=4622290>
##contig=<ID=chr6_cox_hap2,length=4795371>
##contig=<ID=chr6_dbb_hap3,length=4610396>
##contig=<ID=chr6_mann_hap4,length=4683263>
##contig=<ID=chr6_mcf_hap5,length=4833398>
##contig=<ID=chr6_qbl_hap6,length=4611984>
##contig=<ID=chr6_ssto_hap7,length=4928567>
##contig=<ID=chr7_gl000195_random,length=182896>
##contig=<ID=chr8_gl000196_random,length=38914>
##contig=<ID=chr8_gl000197_random,length=37175>
##contig=<ID=chr9_gl000198_random,length=90085>
##contig=<ID=chr9_gl000199_random,length=169874>
##contig=<ID=chr9_gl000200_random,length=187035>
##contig=<ID=chr9_gl000201_random,length=36148>
##contig=<ID=chrUn_gl000211,length=166566>
##contig=<ID=chrUn_gl000212,length=186858>
##contig=<ID=chrUn_gl000213,length=164239>
##contig=<ID=chrUn_gl000214,length=137718>
##contig=<ID=chrUn_gl000215,length=172545>
##contig=<ID=chrUn_gl000216,length=172294>
##contig=<ID=chrUn_gl000217,length=172149>
##contig=<ID=chrUn_gl000218,length=161147>
##contig=<ID=chrUn_gl000219,length=179198>
##contig=<ID=chrUn_gl000220,length=161802>
##contig=<ID=chrUn_gl000221,length=155397>
##contig=<ID=chrUn_gl000222,length=186861>
##contig=<ID=chrUn_gl000223,length=180455>
##contig=<ID=chrUn_gl000224,length=179693>
##contig=<ID=chrUn_gl000225,length=211173>
##contig=<ID=chrUn_gl000226,length=15008>
##contig=<ID=chrUn_gl000227,length=128374>
##contig=<ID=chrUn_gl000228,length=129120>
##contig=<ID=chrUn_gl000229,length=19913>
##contig=<ID=chrUn_gl000230,length=43691>
##contig=<ID=chrUn_gl000231,length=27386>
##contig=<ID=chrUn_gl000232,length=40652>
##contig=<ID=chrUn_gl000233,length=45941>
##contig=<ID=chrUn_gl000234,length=40531>
##contig=<ID=chrUn_gl000235,length=34474>
##contig=<ID=chrUn_gl000236,length=41934>
##contig=<ID=chrUn_gl000237,length=45867>
##contig=<ID=chrUn_gl000238,length=39939>
##contig=<ID=chrUn_gl000239,length=33824>
##contig=<ID=chrUn_gl000240,length=41933>
##contig=<ID=chrUn_gl000241,length=42152>
##contig=<ID=chrUn_gl000242,length=43523>
##contig=<ID=chrUn_gl000243,length=43341>
##contig=<ID=chrUn_gl000244,length=39929>
##contig=<ID=chrUn_gl000245,length=36651>
##contig=<ID=chrUn_gl000246,length=38154>
##contig=<ID=chrUn_gl000247,length=36422>
##contig=<ID=chrUn_gl000248,length=39786>
##contig=<ID=chrUn_gl000249,length=38502>
##ALT=<ID=X,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">

 

 

 

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by bio_vitus0
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