Pileup of mapped diploid
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7 weeks ago
Axzd ▴ 70

Hello, I am mapping a diploid phased assembly on an haploid reference. I would like a tool that naively output all character states for each mapped position. Exactly like you would if you were to record by hands the character states for each position you look at. Bcftools mpileup doesn't work well for that because it outputs likelihood calculation and wild card allele. I don't need that. Any idea? Or it will be a custom htslib exe?

Thanks a lot

diploid Pileup • 204 views
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Entering edit mode
7 weeks ago
Axzd ▴ 70

Answering my own question, would this command work? It seems so, but I always have a little doubt bcftools would do some internal computation I don't want

bcftools mpileup -f ../assembly.fasta H5A2.dual.sorted.bam|bcftools call -m  -A 

This seems to output the genotype for all positon; however since my DP is always 2, will the GT field be trustworthy? Thanks again.

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