Mpileup Multiple Samples - Individual Dp4 Values

Question

[Deniz]

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!!

[Ks-seq]

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

[Arup Ghosh]

Please start a new thread with your question.

Answer 1

[Sean Davis]

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