I have a VCF file and a reference fasta file, and am trying to create a consensus sequence using vcf-consensus.
First I create a tabix file, and then I run
cat NC_002516.2.fa | vcf-consensus 1_e5_d30.vcf.gz > out.fa
and I get an error
The fasta sequence does not match the REF at NC_002516.2:837550. G() in .fa, GT in .vcf at /group/RDI/gatk/vcftools/vcftools_0.1.9/perl/vcf-consensus line 18 main::error('The fasta sequence does not match the REF at NC_002516.2:8375...') called at /group/RDI/gatk/vcftools/vcftools_0.1.9/perl/vcf-consensus line 129 main::apply_variant('HASH(0x13a8b2a0)', 'ARRAY(0x13e1ac70)') called at /group/RDI/gatk/vcftools/vcftools_0.1.9/perl/vcf-consensus line 87 main::do_consensus('HASH(0x13a8b2a0)') called at /group/RDI/gatk/vcftools/vcftools_0.1.9/perl/vcf-consensus line 9
Has anyone else encountered this? Looking at the VCF file for location 837550,
NC_002516.2 521975 . AC A 3149.48 PASS AC=2;AF=1.00;AN=2;DP=79;FS=0.000;HRun=1;HaplotypeScore=315.8867;MQ=59.23;MQ0=0;QD=39.87;SB=-1477.05 GT:AD:DP:GQ:PL 1/1:1,78:79:99:3192,238,0 NC_002516.2 574043 . A AGGG 5241.60 PASS AC=2;AF=1.00;AN=2;DP=78;FS=0.000;HRun=1;HaplotypeScore=335.5748;MQ=42.53;MQ0=0;QD=67.20;SB=-2258.53 GT:AD:DP:GQ:PL 1/1:14,63:78:99:5242,235,0 NC_002516.2 675693 . G A 1670.23 PASS AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=16.7733;MQ=57.48;MQ0=0;QD=24.21;SB=-839.28 GT:AD:DP:GQ:PL 1/1:0,69:69:99:1703,207,0 AC=2;AF=1.00;AN=2;DP=82;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=10.8533;MQ=59.44;MQ0=0;QD=24.28;SB=-814.59 GT:AD:DP:GQ:PL 1/1:0,82:82:99:2024,246,0 NC_002516.2 837550 . GT G 2892.26 PASS AC=2;AF=1.00;AN=2;DP=72;FS=0.000;HRun=1;HaplotypeScore=278.7822;MQ=59.96;MQ0=0;QD=40.17;SB=-1333.27 GT:AD:DP:GQ:PL 1/1:0
837550 is an indel. The thing is, there have been indels before, so that does not look to be the problem. Thanks
are your sure the assembly version your vcf file is based on and the assembly version of your fasta file are the same