Question: Vcf-Consensus To Generate Consensus File
1
gravatar for Nupur G
5.6 years ago by
Nupur G30
Nupur G30 wrote:

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

vcf consensus next-gen • 3.1k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 5.6 years ago by Nupur G30
2

are your sure the assembly version your vcf file is based on and the assembly version of your fasta file are the same

ADD REPLYlink written 5.6 years ago by Laura1.6k
1
gravatar for Nupur G
5.6 years ago by
Nupur G30
Nupur G30 wrote:

Yes I am...I looked in the code, and it seems that it was a QC check that it was failing it. So I commented it. But not sure if that is a good thing.

ADD COMMENTlink written 5.6 years ago by Nupur G30
0
gravatar for liangjiao.xue
3.5 years ago by
liangjiao.xue100
United States
liangjiao.xue100 wrote:

I got the same error of "The fasta sequence does not match the REF", and fixed this problem with dos2unix command

dos2unix NC_002516.2.fa
cat NC_002516.2.fa | vcf-consensus 1_e5_d30.vcf.gz > out.fa

 

ADD COMMENTlink written 3.5 years ago by liangjiao.xue100
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