[Vcftools-help] bcftools consensus trying to apply the alternative allele always that my sample is homozygous or heterozygous alternative for the site

[Eric G. <shi...@gm...>]

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

>10:410-420
Reference             GTAGTT*T*AATT
Pseudoreference GTAGTT*T*AATT

##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


>10:2820-2830
Reference              TTCCT*G*CCTTT
Pseudoreference  TTCCT*T*CCTTT

##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 always
that my sample is heterozygous or homozyguous for the alternative allele?


Best Wishes,


-- 
Eric