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Base call from BAM file

Hi, I have a BAM file and a reference (let's say 1000 genomes data), I would like to extract from the BAM file all the possible overlapping bases with my reference dataset (not only the variants. Basically I would like to perform a base calling and not a variant calling). This extraction should be done according to a random selection of one read per base. Is there any way to do it?

Thanks

bam vcf
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written by Simo • Simo

You could pipe the output of samtools mpileup to a script that randomly selects a single base (no clue why you'd want to do that).

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written by Devon Ryan Devon Ryan

all the possible overlapping bases with my reference dataset

How do you define indel overlap?

I would like to perform a base calling and not a variant calling

How does this differ from setting the flag on your favorite variant caller to also output homozygous reference calls?

This extraction should be done according to a random selection of one read per base.

Why are you downsampling? Why aren't you extracting all read bases that align to any given position and processing that?

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written by d-cameron d-cameron

  • I do not take into account indels.

  • I don't have any experience on this, that's why I was asking for help.

  • I'm working on a low coverage aDNA.

Thanks

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written by Simo • Simo

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