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consensus sequence from BAM file

Hi, I used samtools mpileup -uf chr01.fasta chr01.bam | bcftools call -c | vcfutils.pl vcf2fq > chr01-cns.fastq to make a consensus sequence from BAM file. However, it has used IUPAC characters. How would it be possible to choose a base with the most appearance at locus position rather than IUPAC?

Thank you in advance.

samtools bcftools vcfutils
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written by Ric Ric

I do not care about them.

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written by Ric Ric

So what do you do if a position has 10 reads A and 10 reads C?

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written by WouterDeCoster WouterDeCoster

Good question. What would error correction for PacBio do in this case?

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written by Ric Ric

I think WoulterDeCoster's question was about, what do you do if you have a heterozygous site with a 50/50 distribution.

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written by Gabriel R. Gabriel R.

I do not know what to do with 50/50 distribution. What would error correction for PacBio do in this case?

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written by Ric Ric

Well I hope that any error correction software does not "correct" true het sites :-) Why can't you use a small script that picks an allele at random at UIPAC ambiguous codes?

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written by Gabriel R. Gabriel R.

Hi, I ended up to write a script.

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written by Ric Ric

it this mt or nuclear?

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written by Gabriel R. Gabriel R.

it is nuclear data..

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written by Ric Ric

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