Hello,
I am trying to use the VCFgenotype-to-haplotype tool (from Garrison, E. (2015). vcflib . GitHub repository . GitHub. Retrieved from GitHub - vcflib/vcflib: C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings) on phased vcf data that I obtained from the Michigan imputation server. I receive this message:
“error: more sample fields than samples listed in header
samples:
line: “##FILTER=<ID=PASS,Description=”“All filters passed””>" "
I would like someone’s help in figuring out what to fix in my VCF. I have 130 samples, which is not indicated anywhere in the header. Thanks so much!
Here is the full header:
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description=“All filters passed”>
##picardVersion=Version:2.21.6-SNAPSHOT
##FILTER=<ID=DUPE,Description=“Duplicate assays position.”>
##FILTER=<ID=FAIL_REF,Description=“Assay failed to map to reference.”>
##FILTER=<ID=TRIALLELIC,Description=“Tri-allelic assay.”>
##FILTER=<ID=ZEROED_OUT_ASSAY,Description=“Assay Zeroed out (marked as uncallable) in the Illumina Cluster File”>
##FORMAT=<ID=BAF,Number=1,Type=Float,Description=“B Allele Frequency”>
##FORMAT=<ID=GT,Number=1,Type=String,Description=“Genotype”>
##FORMAT=<ID=GTA,Number=1,Type=String,Description=“Illumina Autocall Genotype”>
##FORMAT=<ID=GTZ,Number=1,Type=String,Description=“zCall Genotype”>
##FORMAT=<ID=IGC,Number=1,Type=Float,Description=“Illumina GenCall Confidence Score”>
##FORMAT=<ID=LRR,Number=1,Type=Float,Description=“Log R Ratio”>
##FORMAT=<ID=NORMX,Number=1,Type=Float,Description=“Normalized X intensity”>
##FORMAT=<ID=NORMY,Number=1,Type=Float,Description=“Normalized Y intensity”>
##FORMAT=<ID=R,Number=1,Type=Float,Description=“Normalized R value”>
##FORMAT=<ID=THETA,Number=1,Type=Float,Description=“Normalized Theta value”>
##FORMAT=<ID=X,Number=1,Type=Integer,Description=“Raw X intensity”>
##FORMAT=<ID=Y,Number=1,Type=Integer,Description=“Raw Y intensity”>
##pipeline=michigan-imputationserver-1.5.7
##phasing=eagle-2.4
##INFO=<ID=AF,Number=A,Type=Float,Description=“Allele Frequency, for each ALT allele, in the same order as listed”>
##INFO=<ID=ALLELE_A,Number=1,Type=String,Description=“A allele”>
##INFO=<ID=ALLELE_B,Number=1,Type=String,Description=“B allele”>
##INFO=<ID=BEADSET_ID,Number=1,Type=Integer,Description=“Bead set ID for normalization”>
##INFO=<ID=GC_SCORE,Number=1,Type=Float,Description=“Gentrain Score”>
##INFO=<ID=ILLUMINA_BUILD,Number=1,Type=String,Description=“Genome Build in Illumina manifest”>
##INFO=<ID=ILLUMINA_CHR,Number=1,Type=String,Description=“Chromosome in Illumina manifest”>
##INFO=<ID=ILLUMINA_POS,Number=1,Type=Integer,Description=“Position in Illumina manifest”>
##INFO=<ID=ILLUMINA_STRAND,Number=1,Type=String,Description=“Probe strand”>
##INFO=<ID=N_AA,Number=1,Type=Integer,Description=“Number of AA calls in training set”>
##INFO=<ID=N_AB,Number=1,Type=Integer,Description=“Number of AB calls in training set”>
##INFO=<ID=N_BB,Number=1,Type=Integer,Description=“Number of BB calls in training set”>
##INFO=<ID=PROBE_A,Number=1,Type=String,Description=“Probe base pair sequence”>
##INFO=<ID=PROBE_B,Number=1,Type=String,Description=“Probe base pair sequence; not missing for strand-ambiguous SNPs”>
##INFO=<ID=SOURCE,Number=1,Type=String,Description=“Probe source”>
##INFO=<ID=devR_AA,Number=1,Type=Float,Description=“Standard deviation of normalized R for AA cluster”>
##INFO=<ID=devR_AB,Number=1,Type=Float,Description=“Standard deviation of normalized R for AB cluster”>
##INFO=<ID=devR_BB,Number=1,Type=Float,Description=“Standard deviation of normalized R for BB cluster”>
##INFO=<ID=devTHETA_AA,Number=1,Type=Float,Description=“Standard deviation of normalized THETA for AA cluster”>
##INFO=<ID=devTHETA_AB,Number=1,Type=Float,Description=“Standard deviation of normalized THETA for AB cluster”>
##INFO=<ID=devTHETA_BB,Number=1,Type=Float,Description=“Standard deviation of normalized THETA for BB cluster”>
##INFO=<ID=devX_AA,Number=1,Type=Float,Description=“Standard deviation of normalized X for AA cluster”>
##INFO=<ID=devX_AB,Number=1,Type=Float,Description=“Standard deviation of normalized X for AB cluster”>
##INFO=<ID=devX_BB,Number=1,Type=Float,Description=“Standard deviation of normalized X for BB cluster”>
##INFO=<ID=devY_AA,Number=1,Type=Float,Description=“Standard deviation of normalized Y for AA cluster”>
##INFO=<ID=devY_AB,Number=1,Type=Float,Description=“Standard deviation of normalized Y for AB cluster”>
##INFO=<ID=devY_BB,Number=1,Type=Float,Description=“Standard deviation of normalized Y for BB cluster”>
##INFO=<ID=meanR_AA,Number=1,Type=Float,Description=“Mean of normalized R for AA cluster”>
##INFO=<ID=meanR_AB,Number=1,Type=Float,Description=“Mean of normalized R for AB cluster”>
##INFO=<ID=meanR_BB,Number=1,Type=Float,Description=“Mean of normalized R for BB cluster”>
##INFO=<ID=meanTHETA_AA,Number=1,Type=Float,Description=“Mean of normalized THETA for AA cluster”>
##INFO=<ID=meanTHETA_AB,Number=1,Type=Float,Description=“Mean of normalized THETA for AB cluster”>
##INFO=<ID=meanTHETA_BB,Number=1,Type=Float,Description=“Mean of normalized THETA for BB cluster”>
##INFO=<ID=meanX_AA,Number=1,Type=Float,Description=“Mean of normalized X for AA cluster”>
##INFO=<ID=meanX_AB,Number=1,Type=Float,Description=“Mean of normalized X for AB cluster”>
##INFO=<ID=meanX_BB,Number=1,Type=Float,Description=“Mean of normalized X for BB cluster”>
##INFO=<ID=meanY_AA,Number=1,Type=Float,Description=“Mean of normalized Y for AA cluster”>
##INFO=<ID=meanY_AB,Number=1,Type=Float,Description=“Mean of normalized Y for AB cluster”>
##INFO=<ID=meanY_BB,Number=1,Type=Float,Description=“Mean of normalized Y for BB cluster”>
##INFO=<ID=refSNP,Number=1,Type=String,Description=“dbSNP rsID”>
##INFO=<ID=zthresh_X,Number=1,Type=Float,Description=“zCall X threshold”>
##INFO=<ID=zthresh_Y,Number=1,Type=Float,Description=“zCall Y threshold”>
##arrayType=GSAMD-24v1-0_20011747_A1
##autocallVersion=3.0.0
##clusterFile=GSAMD-24v1-0_20011747_A1.egt
##content=GSAMD-24v1-0_20011747_A1.1.3.extended.csv
##contig=<ID=1,assembly=GRCh37,length=249250621>
##contig=<ID=2,assembly=GRCh37,length=243199373>
##contig=<ID=3,assembly=GRCh37,length=198022430>
##contig=<ID=4,assembly=GRCh37,length=191154276>
##contig=<ID=5,assembly=GRCh37,length=180915260>
##contig=<ID=6,assembly=GRCh37,length=171115067>
##contig=<ID=7,assembly=GRCh37,length=159138663>
##contig=<ID=8,assembly=GRCh37,length=146364022>
##contig=<ID=9,assembly=GRCh37,length=141213431>
##contig=<ID=10,assembly=GRCh37,length=135534747>
##contig=<ID=11,assembly=GRCh37,length=135006516>
##contig=<ID=12,assembly=GRCh37,length=133851895>
##contig=<ID=13,assembly=GRCh37,length=115169878>
##contig=<ID=14,assembly=GRCh37,length=107349540>
##contig=<ID=15,assembly=GRCh37,length=102531392>
##contig=<ID=16,assembly=GRCh37,length=90354753>
##contig=<ID=17,assembly=GRCh37,length=81195210>
##contig=<ID=18,assembly=GRCh37,length=78077248>
##contig=<ID=19,assembly=GRCh37,length=59128983>
##contig=<ID=20,assembly=GRCh37,length=63025520>
##contig=<ID=21,assembly=GRCh37,length=48129895>
##contig=<ID=22,assembly=GRCh37,length=51304566>
##contig=<ID=X,assembly=GRCh37,length=155270560>
##contig=<ID=Y,assembly=GRCh37,length=59373566>
##contig=<ID=MT,assembly=GRCh37,length=16569>
##contig=<ID=GL000207.1,assembly=GRCh37,length=4262>
##contig=<ID=GL000226.1,assembly=GRCh37,length=15008>
##contig=<ID=GL000229.1,assembly=GRCh37,length=19913>
##contig=<ID=GL000231.1,assembly=GRCh37,length=27386>
##contig=<ID=GL000210.1,assembly=GRCh37,length=27682>
##contig=<ID=GL000239.1,assembly=GRCh37,length=33824>
##contig=<ID=GL000235.1,assembly=GRCh37,length=34474>
##contig=<ID=GL000201.1,assembly=GRCh37,length=36148>
##contig=<ID=GL000247.1,assembly=GRCh37,length=36422>
##contig=<ID=GL000245.1,assembly=GRCh37,length=36651>
##contig=<ID=GL000197.1,assembly=GRCh37,length=37175>
##contig=<ID=GL000203.1,assembly=GRCh37,length=37498>
##contig=<ID=GL000246.1,assembly=GRCh37,length=38154>
##contig=<ID=GL000249.1,assembly=GRCh37,length=38502>
##contig=<ID=GL000196.1,assembly=GRCh37,length=38914>
##contig=<ID=GL000248.1,assembly=GRCh37,length=39786>
##contig=<ID=GL000244.1,assembly=GRCh37,length=39929>
##contig=<ID=GL000238.1,assembly=GRCh37,length=39939>
##contig=<ID=GL000202.1,assembly=GRCh37,length=40103>
##contig=<ID=GL000234.1,assembly=GRCh37,length=40531>
##contig=<ID=GL000232.1,assembly=GRCh37,length=40652>
##contig=<ID=GL000206.1,assembly=GRCh37,length=41001>
##contig=<ID=GL000240.1,assembly=GRCh37,length=41933>
##contig=<ID=GL000236.1,assembly=GRCh37,length=41934>
##contig=<ID=GL000241.1,assembly=GRCh37,length=42152>
##contig=<ID=GL000243.1,assembly=GRCh37,length=43341>
##contig=<ID=GL000242.1,assembly=GRCh37,length=43523>
##contig=<ID=GL000230.1,assembly=GRCh37,length=43691>
##contig=<ID=GL000237.1,assembly=GRCh37,length=45867>
##contig=<ID=GL000233.1,assembly=GRCh37,length=45941>
##contig=<ID=GL000204.1,assembly=GRCh37,length=81310>
##contig=<ID=GL000198.1,assembly=GRCh37,length=90085>
##contig=<ID=GL000208.1,assembly=GRCh37,length=92689>
##contig=<ID=GL000191.1,assembly=GRCh37,length=106433>
##contig=<ID=GL000227.1,assembly=GRCh37,length=128374>
##contig=<ID=GL000228.1,assembly=GRCh37,length=129120>
##contig=<ID=GL000214.1,assembly=GRCh37,length=137718>
##contig=<ID=GL000221.1,assembly=GRCh37,length=155397>
##contig=<ID=GL000209.1,assembly=GRCh37,length=159169>
##contig=<ID=GL000218.1,assembly=GRCh37,length=161147>
##contig=<ID=GL000220.1,assembly=GRCh37,length=161802>
##contig=<ID=GL000213.1,assembly=GRCh37,length=164239>
##contig=<ID=GL000211.1,assembly=GRCh37,length=166566>
##contig=<ID=GL000199.1,assembly=GRCh37,length=169874>
##contig=<ID=GL000217.1,assembly=GRCh37,length=172149>
##contig=<ID=GL000216.1,assembly=GRCh37,length=172294>
##contig=<ID=GL000215.1,assembly=GRCh37,length=172545>
##contig=<ID=GL000205.1,assembly=GRCh37,length=174588>
##contig=<ID=GL000219.1,assembly=GRCh37,length=179198>
##contig=<ID=GL000224.1,assembly=GRCh37,length=179693>
##contig=<ID=GL000223.1,assembly=GRCh37,length=180455>
##contig=<ID=GL000195.1,assembly=GRCh37,length=182896>
##contig=<ID=GL000212.1,assembly=GRCh37,length=186858>
##contig=<ID=GL000222.1,assembly=GRCh37,length=186861>
##contig=<ID=GL000200.1,assembly=GRCh37,length=187035>
##contig=<ID=GL000193.1,assembly=GRCh37,length=189789>
##contig=<ID=GL000194.1,assembly=GRCh37,length=191469>
##contig=<ID=GL000225.1,assembly=GRCh37,length=211173>
##contig=<ID=GL000192.1,assembly=GRCh37,length=547496>
##contig=<ID=NC_007605,assembly=NC_007605.1,length=171823>
##extendedIlluminaManifestVersion=1.3
##extendedManifestFile=GSAMD-24v1-0_20011747_A1.1.3.extended.csv
##manifestFile=GSAMD-24v1-0_20011747_A1.bpm
##picardVersion=Version:2.22.0-SNAPSHOT
##reference=/cromwell_root/gcp-public-data–broad-references/hg19/v0/Homo_sapiens_assembly19.fasta
##source=GtcToVcf
##zcallThresholds=GSAMD-24v1-0_20011747_A1.egt.thresholds.txt
##zcallVersion=1.0.0.0
##source_20200707.1=vcf-merge(r953) Bujakowska_Pierce_MEEI_GSA_128-samples_03302020.vcf.gz Bujakowska_Pierce_MEEI_GSA_2-samples_06-22-20.vcf.gz
##sourceFiles_20200707.1=0:Bujakowska_Pierce_MEEI_GSA_128-samples_03302020.vcf.gz,1:Bujakowska_Pierce_MEEI_GSA_2-samples_06-22-20.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description=“Source File (index to sourceFiles, f when filtered)”>
##INFO=<ID=AC,Number=.,Type=Integer,Description=“Allele count in genotypes”>
##INFO=<ID=AN,Number=1,Type=Integer,Description=“Total number of alleles in called genotypes”>
##eagleVersion=2.4+htslib-1.4