Hi,
I am trying to perform variant calling for detection of polymorphism in
difference crop varieties.
I am using samtools mpileup and the resulting output is in vcf format.
Thereafter, I call the variants using bcftools call function and index the
output. However, when I use the bcftools consensus to generate a consensus,
my desired output (in FASTA format) seem not to make sense. For instance,
at a particular position (1), the Alternative allele is A with a depth of 7
while the Reference allele is C. In the consensus, the reported allele is
that of reference instead of the alternative allele. How can ensure that
for each position where there is a SNP, extract the allele that occurs at a
higher percentage. Here are the commands i use:
samtools mpileup -f Cas.cds.fa -A -v -o Nam.sorted.vcf Nam.sorted.bam
bcftools call -c -Oz -o Nam.sorted Nam.sorted.vcf
bcftools index Nam.sorted
bcftools consensus -f Cas.cds.fa Nam.sorted > Nam_consensus.txt
Regards,
John
--
*John Juma*
LinkedIn <https://www.linkedin.com/in/john-juma>
KE +254 723 585 016
SK @john_juma99
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