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:
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
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:
Code:
samtools mpileup -d 1000000 -I -f in_genome.fasta 1st.bam 2nd.bam ... > out.mpileup
I am using samtools version 0.1.19
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