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How can I be sure that the mpileup result is correct, and what is the reasons for the incorrect results of mpileup command of SAMtools

Hi everyone,

I am using samtools to make a mpileup file for three samples, and I am using the 1000 genome project data set. Firstly, I want to know how I can make sure that the resulting mpileup file is correct. Secondly, in case of the incorrect result, what could be the reasons for this incorrect mpileup file if?

I am using the ubuntu bash on win 10, and my samtool command is: 

$ samtools mpileup -B -q 1 -f build37.fa HG00403.bam HG00404.bam HG00405.bam >trio.mpileup
next-gen alignment software error snp
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written by hamid.khape • hamid.khape

Please define what you mean by correct.

• 0 views • link
written by ATpoint ATpoint

I mean the expected output. I mean how I can make sure that some thing is not wrong with the mpileup output.

After the mpileup command, I am doing some analyses with VarScan. Unfortunately, the output is not what it should be. Therefore, I want to know what could be wrong here.

By the way, I am using the commands indicated in their website, so the commands and their values are ok.

Let me give you another example: 

samtools mpileup -B -f build37.fa HG00405.bam | java -jar varscan.jar mpileup2snp

I am using the above command, but the output is 0 SNPs which is an incorrect output. The output of the command

How can I find out what is wrong here?

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written by hamid.khape • hamid.khape

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