##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=LowQual,Description="Low quality">
##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=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=HaplotypeCaller,CommandLine="HaplotypeCaller --sample-ploidy 1 --min-base-quality-score 20 --output ERR4145453.gatk.vcf --input ERR4145453.preprocessed.bam --reference /home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa --minimum-mapping-quality 20 --annotation AlleleFraction --use-posteriors-to-calculate-qual false --dont-use-dragstr-priors false --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --num-reference-samples-if-no-call 0 --genotype-assignment-method USE_PLS_TO_ASSIGN --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --dragen-mode false --apply-bqd false --apply-frd false --disable-spanning-event-genotyping false --transform-dragen-mapping-quality false --mapping-quality-threshold-for-genotyping 20 --max-effective-depth-adjustment-for-frd 0 --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --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 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 0 --force-call-filtered-alleles false --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming 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 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.2.0.0",Date="October 19, 2021 8:45:22 PM CEST">
##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=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##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=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=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##contig=<ID=MN908947.3,length=29903>
##source=HaplotypeCaller
##INFO=<ID=OLD_CLUMPED,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
##bcftools_normVersion=1.12+htslib-1.12
##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Tue Oct 19 20:45:37 2021
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="ID for set of phased genotypes">
##bcftools_normCommand=norm --rm-dup exact -o ERR4145453.gatk.normalized.vcf -; Date=Tue Oct 19 20:45:37 2021
##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -noStats -no-downstream -no-upstream -no-intergenic -no-intron -noShiftHgvs Sars_cov_2.ASM985889v3.101 ERR4145453.gatk.normalized.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=CONS_HMM_SARS_COV_2,Number=1,Type=Float,Description="Mutation depletion score track based on significant enrichment/depletion of nonsingleton SARS-CoV-2 mutations (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateVersion=1.12+htslib-1.12
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_SARS_COV_2 --output-type z -; Date=Tue Oct 19 20:45:42 2021
##INFO=<ID=CONS_HMM_SARBECOVIRUS,Number=1,Type=Float,Description="30 ConsHMM conservation states learned from the Sarbecovirus sequence alignment (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionSarbecovirusConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionSarbecovirusConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_SARBECOVIRUS --output-type z -; Date=Tue Oct 19 20:45:42 2021
##INFO=<ID=CONS_HMM_VERTEBRATE_COV,Number=1,Type=Float,Description="30 ConsHMM conservation states learned from the vertebrate CoV sequence alignment (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionVertebrateCoVConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionVertebrateCoVConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_VERTEBRATE_COV --output-type z -; Date=Tue Oct 19 20:45:42 2021
##INFO=<ID=PFAM_NAME,Number=.,Type=String,Description="Pfam domain name as reported in Ensembl annotations">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_names.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_names.header.txt -c CHROM,FROM,TO,PFAM_NAME --output-type z -; Date=Tue Oct 19 20:45:42 2021
##INFO=<ID=PFAM_DESCRIPTION,Number=.,Type=String,Description="Pfam domain description as reported in Ensembl annotations">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_descriptions.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_descriptions.header.txt -c CHROM,FROM,TO,PFAM_DESCRIPTION --output-type z -; Date=Tue Oct 19 20:45:42 2021
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	ERR4145453
MN908947.3	241	.	C	T	237.04	.	AC=1;AF=1;AN=1;DP=8;FS=0;MLEAC=1;MLEAF=1;MQ=60;QD=25.36;SOR=0.693;CONS_HMM_SARS_COV_2=-1.25436;CONS_HMM_SARBECOVIRUS=-1.25436;CONS_HMM_VERTEBRATE_COV=0	GT:AD:AF:DP:GQ:PL	1:0,6:1:6:99:247,0
MN908947.3	3037	.	C	T	6976.04	.	AC=1;AF=1;AN=1;DP=175;FS=0;MLEAC=1;MLEAF=1;MQ=60;QD=28.73;SOR=0.728;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2772C>T|p.F924F|2772/21290|2772/21290|924/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_N_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, N-terminal, betacoronavirus	GT:AD:AF:DP:GQ:PL	1:0,171:1:171:99:6986,0
MN908947.3	14408	.	C	T	4569.04	.	AC=1;AF=1;AN=1;DP=111;FS=0;MLEAC=1;MLEAF=1;MQ=60;QD=30.97;SOR=0.846;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14143C>T|p.L4715L|14143/21290|14143/21290|4715/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral	GT:AD:AF:DP:GQ:PL	1:0,110:1:110:99:4579,0
MN908947.3	21784	.	T	G	5248.04	.	AC=1;AF=1;AN=1;BaseQRankSum=-0.426;DP=141;FS=9.859;MLEAC=1;MLEAF=1;MQ=59.99;MQRankSum=0.036;QD=27.24;ReadPosRankSum=-0.085;SOR=0.353;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.222T>G|p.N74K|222/3822|222/3822|74/1273||;CONS_HMM_SARS_COV_2=-0.80744;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.80744;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal	GT:AD:AF:DP:GQ:PL	1:3,128:0.977:131:99:5258,0
MN908947.3	21846	.	C	T	384.04	.	AC=1;AF=1;AN=1;BaseQRankSum=1.841;DP=110;FS=0;MLEAC=1;MLEAF=1;MQ=60.1;MQRankSum=-1.049;QD=3.59;ReadPosRankSum=-0.971;SOR=0.709;ANN=T|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.284C>T|p.T95I|284/3822|284/3822|95/1273||;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal	GT:AD:AF:DP:GQ:PL	1:50,57:0.533:107:99:394,0
MN908947.3	23403	.	A	G	9984.04	.	AC=1;AF=1;AN=1;BaseQRankSum=2.481;DP=261;FS=2.061;MLEAC=1;MLEAF=1;MQ=60;MQRankSum=0;QD=28.2;ReadPosRankSum=2.858;SOR=0.23;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1841A>G|p.D614G|1841/3822|1841/3822|614/1273||;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0	GT:AD:AF:DP:GQ:PL	1:4,246:0.984:250:99:9994,0