Hi all

I am using bcftools consensus to add the alternative SNPs to a fasta file.

I am running it in two ways:

bcftools consensus -i -s sample1 -f reference.fasta file.vcf.gz > pseudoreference.fasta

bcftools consensus -H A -s sample1 -f reference.fasta file.vcf.gz > pseudoreference2.fasta

With my first command line to run bcftools, I get the alternative allele in the new fasta only when my sample is homozygous alternative. Below is an example of that where I show the SNP region and the SNP position highlighted in bold and the vcf line of the SNP with the sample info highlighted in bold also.

position 10:410-420

Reference:            GTAGTTTAATT

Pseudoreference   GTAGTTTAATT

VCF region

10 416 . T C 548.44 PASS AC=2;AF=0.500;AN=4;BaseQRankSum=2.10;ClippingRankSum=0.367;DP=36;ExcessHet=4.7712;FS=32.570;MLEAC=2;MLEAF=0.500;MQ=44.99;MQRankSum=-2.196e+00;QD=15.23;ReadPosRankSum=-1.220e-01;SOR=5.669 GT:AD:DP:GQ:PL 0/1:10,9:19:99:325,0,319 0/1:10,7:17:99:252,0,259

position 10:2820-2830

Reference           TTCCTGCCTTT

Pseudoreference TTCCTTCCTTT

VCF region

10 2825 . G T 253.54 PASS AC=3;AF=0.750;AN=4;BaseQRankSum=-6.840e-01;ClippingRankSum=0.322;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=43.74;MQRankSum=-6.840e-01;QD=21.13;ReadPosRankSum=-9.560e-01;SOR=0.495 GT:AD:DP:GQ:PL 1/1:0,4:4:12:164,12,0 0/1:3,5:8:99:119,0,104

I would like to have always the alternative SNP even if the sample is heterozygous so I try the second bcftools script that is above and the result is the next error:

Can't apply 17-th haplotype at 10:416

Do you know how I can add to my fasta always the alternative allele if my sample is heterozygous or homozyguous for the alternative allele?

Best Wishes,