mpileup and multiple input files

[Axel]

Hi All,

Is there any reason why the order in which .bam files are given to mpileup would affect the number of sites in the mpileup file?

I have 8 .bam files and I need to have an mpileup file with the samples in a particular order in the columns. I have run mpileup twice with the following settings:

samtools mpileup -d 1000000 -I -f in_genome.fasta 1st.bam 2nd.bam ... > out.mpileup

When I run it again with a different order of the input .bam files I get a massively different mpileup file that then affects how many SNPs are called/analysed downstream.

I am using samtools version 0.1.19

[jkbonfield]

I've no idea, but you should use samtools-1.2 as 0.1.19 is pretty ancient now.

[Axel]

Thanks jkbonfield. I'll try updating in case it's just a version issue. Still seems like odd behaviour though.

[Axel]

I have now tried with the newer version of samtools (v. 1.2). This at least gives me mpileup files that are the same size. Hopefully this was just a weird version bug. We'll see what the downstream analyses turn up.