Question: getting sequence by combining reference and variants (fasta and vcf files)
0
gravatar for Lin
21 months ago by
Lin10
United States
Lin10 wrote:

Is there a tool that will incorporate the variants into a reference genome based on the genotype information (GT info) and the allele depth (AD info)?

So, for loci where there is a variant, the tool will look at the genotype, if it is heterozygous it will take allele with highest allelic depth and incorporate it to reference genome? If it is homozygous it will take the allele indicated in the GT info and incorporate it to reference genome.

Example heterozygous:

reference sequence: AGG 
vcf: 
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S6 
20 2 G GAG,GAA 626.73 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.85;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=29.87;SOR=4.977;VQSLOD=1.17;culprit=SOR GT:AD:DP:GQ:PL 1/2:0,4,70:11:99:664,307,281,182,0,147

The new sequence will be: AGAAG

Example homozygous:

reference sequence: AGG
vcf:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S6
20 2 G GAG,GAA 626.73 PASS AC=1,1;AF=0.500,0.500;AN=2;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.85;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=29.87;SOR=4.977;VQSLOD=1.17;culprit=SOR GT:AD:DP:GQ:PL 1/1:0,7,0:11:99:664,307,281,182,0,147

the new sequence will be:
AGAGG
snp mutation sequence genome vcf • 702 views
ADD COMMENTlink modified 21 months ago by WouterDeCoster31k • written 21 months ago by Lin10
0
gravatar for WouterDeCoster
21 months ago by
Belgium
WouterDeCoster31k wrote:

This probably isn't a complete answer to your question but it might be a start: GATK FastaAlternateReferenceMaker

ADD COMMENTlink written 21 months ago by WouterDeCoster31k

GATK FastaAlternateReferenceMaker select the allele randomly. There is no option to select the allele based on allelic depth.

ADD REPLYlink written 21 months ago by Lin10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1369 users visited in the last hour