GATK 4.1.1.0 GenomicsDBImport error : Duplicate fields exist in vid attribute "fields" and The provided VCF file is malformed at approximately and there aren't enough columns for line

Hello GATK team!

I am currently using Mutect2 & FilterMutectCalls & GenomicsDBImport for somatic calling. In the steps of Mutect2 & FilterMutectCalls, I got samples' gVCF fine. However, I want to use GenomicsDBImport to combine all gVCF and this step is not working with several errors and I am running out of ideas.

GATK4.1.1.0
1: Mutect2 .bam to .g.vcf, seems ok and generate .vcf, .vcf.idx and .vcf.stats

gatk Mutect2 --reference .../hg19.fa --input ....bam --output ...g.vcf -ERC GVCF --tmp-dir ...

2: FilterMutectCalls .g.vcf to .g.vcf, seems ok and generate .vcf, .vcf.idx and .vcf.filteringStats.tsv

gatk FilterMutectCalls --reference .../hg19.fa --variant ...g.vcf --intervals ...hg19.bed --output ...g.vcf --tmp-dir ...

3. When combination:

gatk GenomicsDBImport --reference .../hg19.fa --sample-name-map ${sample_mapFile} --validate-sample-name-map true --intervals ...hg19.bed --genomicsdb-workspace-path ... --max-num-intervals-to-import-in-parallel 20 --consolidate true --batch-size 100 --merge-input-intervals true --tmp-dir ...

This commend is same and ok at germline pipline. VCF files can also be read now. But got this error:

Duplicate field name TLOD found in vid attribute "fields"
Duplicate field name TLOD found in vid attribute "fields"
terminate called after throwing an instance of 'FileBasedVidMapperException'
terminate called recursively
what(): FileBasedVidMapperException : Duplicate fields exist in vid attribute "fields"

4. I deleted this line and re-run:
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log odds ratio score for variant">
Then got this error:

htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 171: . is not a valid start position in the VCF format, for input source: file:///home/yb87626/breast/variantCalling/SRR8437498.postM2.g.vcf
at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:797)
at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:324)
at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:299)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:277)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:64)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:70)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:37)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:486)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.<init>(TribbleIndexedFeatureReader.java:426)
at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:297)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport$1.query(GenomicsDBImport.java:724)
at org.genomicsdb.importer.GenomicsDBImporter.<init>(GenomicsDBImporter.java:146)
at org.genomicsdb.importer.GenomicsDBImporter.lambda$null$2(GenomicsDBImporter.java:573)
at java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1590)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

5. I deleted this line and re-run:
##tumor_sample=SAMN10735600
Then got this error:

[July 3, 2019 7:10:52 AM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1243086848
htsjdk.tribble.TribbleException: Line 169: there aren't enough columns for line END=17447;STRANDQ=93 GT:DP:MIN_DP:TLOD 0/0:1:1:-4.765e-01 (we expected 9 tokens, and saw 3 ), for input source: file:///home/yb87626/breast/variantCalling/SRR8437498.postM2.g.vcf
at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:296)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:277)
at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:64)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:70)
at htsjdk.tribble.AsciiFeatureCodec.decode(AsciiFeatureCodec.java:37)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:486)
at htsjdk.tribble.TribbleIndexedFeatureReader$QueryIterator.<init>(TribbleIndexedFeatureReader.java:426)
at htsjdk.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:297)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport$1.query(GenomicsDBImport.java:724)
at org.genomicsdb.importer.GenomicsDBImporter.<init>(GenomicsDBImporter.java:146)
at org.genomicsdb.importer.GenomicsDBImporter.lambda$null$2(GenomicsDBImporter.java:573)
at java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1590)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

You can see the program recognize 'END=17447;STRANDQ=93 GT:DP:MIN_DP:TLOD 0/0:1:1:-4.765e-01' as a line, but there are columns before them in the same line. The problem may not be this line, because same problem happens at the next line when I delete this line.

Now, I don't know how to solve it. And did I do right before 4 and 5?

Part of .g.vcf:

##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=base_qual,Description="alt median base quality">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=contamination,Description="contamination">
##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">
##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">
##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">
##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">
##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">
##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">
##FILTER=<ID=normal_artifact,Description="artifact_in_normal">
##FILTER=<ID=numt_chimera,Description="NuMT variant with too many ALT reads originally from autosome">
##FILTER=<ID=numt_novel,Description="Alt depth is below expected coverage of NuMT in autosome">
##FILTER=<ID=orientation,Description="orientation bias detected by the orientation bias mixture model">
##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
##FILTER=<ID=position,Description="median distance of alt variants from end of reads">
##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">
##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
##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=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##FORMAT=<ID=TLOD,Number=A,Type=Float,Description="Log odds ratio score for variant">
##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output /home/yb87626/3-6/intermediate/SRR8437498.postM2.g.vcf --variant /home/yb87626/3-6/intermediate/SRR8437498.postM2.raw.g.vcf --intervals /home/yb87626/reference/hg19/corePromoter.hg19.bed --reference /home/yb87626/reference/hg19/hg19.fa --tmp-dir /home/yb87626/3-6/tmp --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --min-reads-per-strand 0 --autosomal-coverage 0.0 --max-numt-fraction 0.85 --min-allele-fraction 0.0 --contamination-estimate 0.0 --log10-somatic-snv-prior -6.0 --log10-somatic-indel-prior -7.0 --initial-artifact-prior -1.0 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.1.0",Date="July 3, 2019 6:46:48 AM UTC">
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --emit-ref-confidence GVCF --output /home/yb87626/3-6/intermediate/SRR8437498.postM2.raw.g.vcf --input /home/yb87626/3-6/intermediate/SRR8437498.bqsr_recalibrated.bam --reference /home/yb87626/reference/hg19/hg19.fa --tmp-dir /home/yb87626/3-6/tmp --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --max-mnp-distance 1 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --genotype-filtered-alleles false --disable-adaptive-pruning false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 1.0 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.1.0",Date="July 2, 2019 4:13:47 PM UTC">
##GVCFBlock-10--5=minGQ=-10(inclusive),maxGQ=-5(exclusive)
##GVCFBlock-15--10=minGQ=-15(inclusive),maxGQ=-10(exclusive)
##GVCFBlock-20--15=minGQ=-20(inclusive),maxGQ=-15(exclusive)
##GVCFBlock-2147483648--25=minGQ=-2147483648(inclusive),maxGQ=-25(exclusive)
##GVCFBlock-25--20=minGQ=-25(inclusive),maxGQ=-20(exclusive)
##GVCFBlock-5-0=minGQ=-5(inclusive),maxGQ=0(exclusive)
##GVCFBlock0-5=minGQ=0(inclusive),maxGQ=5(exclusive)
##GVCFBlock10-2147483647=minGQ=10(inclusive),maxGQ=2147483647(exclusive)
##GVCFBlock5-10=minGQ=5(inclusive),maxGQ=10(exclusive)
##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality">
##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log odds of artifact in normal with same allele fraction as tumor">
##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal LOD score">
##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative-log-10 population allele frequencies of alt alleles">
##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
##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=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log odds ratio score for variant">
##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site">
##MutectVersion=2.2
##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=chrX,length=155270560>
##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=chr20,length=63025520>
##contig=<ID=chrY,length=59373566>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr6_ssto_hap7,length=4928567>
##contig=<ID=chr6_mcf_hap5,length=4833398>
##contig=<ID=chr6_cox_hap2,length=4795371>
##contig=<ID=chr6_mann_hap4,length=4683263>
##contig=<ID=chr6_apd_hap1,length=4622290>
##contig=<ID=chr6_qbl_hap6,length=4611984>
##contig=<ID=chr6_dbb_hap3,length=4610396>
##contig=<ID=chr17_ctg5_hap1,length=1680828>
##contig=<ID=chr4_ctg9_hap1,length=590426>
##contig=<ID=chr1_gl000192_random,length=547496>
##contig=<ID=chrUn_gl000225,length=211173>
##contig=<ID=chr4_gl000194_random,length=191469>
##contig=<ID=chr4_gl000193_random,length=189789>
##contig=<ID=chr9_gl000200_random,length=187035>
##contig=<ID=chrUn_gl000222,length=186861>
##contig=<ID=chrUn_gl000212,length=186858>
##contig=<ID=chr7_gl000195_random,length=182896>
##contig=<ID=chrUn_gl000223,length=180455>
##contig=<ID=chrUn_gl000224,length=179693>
##contig=<ID=chrUn_gl000219,length=179198>
##contig=<ID=chr17_gl000205_random,length=174588>
##contig=<ID=chrUn_gl000215,length=172545>
##contig=<ID=chrUn_gl000216,length=172294>
##contig=<ID=chrUn_gl000217,length=172149>
##contig=<ID=chr9_gl000199_random,length=169874>
##contig=<ID=chrUn_gl000211,length=166566>
##contig=<ID=chrUn_gl000213,length=164239>
##contig=<ID=chrUn_gl000220,length=161802>
##contig=<ID=chrUn_gl000218,length=161147>
##contig=<ID=chr19_gl000209_random,length=159169>
##contig=<ID=chrUn_gl000221,length=155397>
##contig=<ID=chrUn_gl000214,length=137718>
##contig=<ID=chrUn_gl000228,length=129120>
##contig=<ID=chrUn_gl000227,length=128374>
##contig=<ID=chr1_gl000191_random,length=106433>
##contig=<ID=chr19_gl000208_random,length=92689>
##contig=<ID=chr9_gl000198_random,length=90085>
##contig=<ID=chr17_gl000204_random,length=81310>
##contig=<ID=chrUn_gl000233,length=45941>
##contig=<ID=chrUn_gl000237,length=45867>
##contig=<ID=chrUn_gl000230,length=43691>
##contig=<ID=chrUn_gl000242,length=43523>
##contig=<ID=chrUn_gl000243,length=43341>
##contig=<ID=chrUn_gl000241,length=42152>
##contig=<ID=chrUn_gl000236,length=41934>
##contig=<ID=chrUn_gl000240,length=41933>
##contig=<ID=chr17_gl000206_random,length=41001>
##contig=<ID=chrUn_gl000232,length=40652>
##contig=<ID=chrUn_gl000234,length=40531>
##contig=<ID=chr11_gl000202_random,length=40103>
##contig=<ID=chrUn_gl000238,length=39939>
##contig=<ID=chrUn_gl000244,length=39929>
##contig=<ID=chrUn_gl000248,length=39786>
##contig=<ID=chr8_gl000196_random,length=38914>
##contig=<ID=chrUn_gl000249,length=38502>
##contig=<ID=chrUn_gl000246,length=38154>
##contig=<ID=chr17_gl000203_random,length=37498>
##contig=<ID=chr8_gl000197_random,length=37175>
##contig=<ID=chrUn_gl000245,length=36651>
##contig=<ID=chrUn_gl000247,length=36422>
##contig=<ID=chr9_gl000201_random,length=36148>
##contig=<ID=chrUn_gl000235,length=34474>
##contig=<ID=chrUn_gl000239,length=33824>
##contig=<ID=chr21_gl000210_random,length=27682>
##contig=<ID=chrUn_gl000231,length=27386>
##contig=<ID=chrUn_gl000229,length=19913>
##contig=<ID=chrM,length=16571>
##contig=<ID=chrUn_gl000226,length=15008>
##contig=<ID=chr18_gl000207_random,length=4262>
##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.
##source=FilterMutectCalls
##source=Mutect2
##tumor_sample=SAMN10735589
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMN10735589
chr1 1 . N <NON_REF> . PASS END=17405;STRANDQ=93 GT:DP:MIN_DP:TLOD 0/0:0:0:0.00
chr1 17406 . C <NON_REF> . PASS END=17447;STRANDQ=93 GT:DP:MIN_DP:TLOD 0/0:1:1:-4.765e-01
chr1 17448 . A <NON_REF> . PASS END=17448;STRANDQ=93 GT:DP:MIN_DP:TLOD 0/0:2:2:0.669
chr1 17449 . C <NON_REF> . PASS END=17451;STRANDQ=93 GT:DP:MIN_DP:TLOD 0/0:2:1:-4.765e-01