Mpileup Multiple Samples - Individual Dp4 Values · Biostar

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Mpileup Multiple Samples - Individual Dp4 Values

Hi,

I am calling SNP from multiple individuals using mpileup. I was wondering whether it is possible to get DP4 and AF1 values for each individual? I currently have DP4 and AF1 values for the combined dataset, but would like them for each individual as well.I would like to just compare DP4 values of each sample.

Thanks for your ideas!!

vcf samtools

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updated 6.4 years ago by Ks-seq •

• written 14.8 years ago by Deniz •

Any solution? I have same problem, samtools mpileup on multiple samples bam files and cant get DP for each bam file. Can even get with bcftools mpileup. Appreciating reply. Thanks

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written 6.4 years ago by Ks-seq •

Please start a new thread with your question.

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written 6.4 years ago by Arup Ghosh

1 answer

Not DP4, but DP. See the -D flag for samtools mpileup.

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written 14.8 years ago by Sean Davis

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