Hello, I'm working on an GBS analysis workflow which was previously designed for command line usage. It should analyse more than 50 samples. Steps:
- Trimming of fastq-input
- Mapping =>multiple sorted and indexed BAM files, one per sample
My problem starts here:
I want to use the BAM files as input for variant detection in samtools mpileup. On command line, I simply read the path of all BAM files I have created in the previous steps to a list of BAM files and hand this file to mpileup using the -b bamlist.txt option. Doing so, I receive one VCF file storing information of multiple samples I completely failed to reproduce this result in Galaxy. The only way..so far..is to state every BAM file using the mpileup interface "by hand". This will produce the desired file. With two files I got the following Log file
[mpileup] 2 samples in 2 input files <mpileup> Set max per-file depth to 4000
But it is not practicable for more than 10 samples...
So far, I tried Galaxys "multiple input" option as well as the "data list collection" - still every BAM input is treated as a single input file resulting in one VCF per BAM instead of one VCF covering multiple samples.
Anybody here who went into the same problems and knows the trick? Is there a possibility to hand over BAM input to mpileup dynamically?
Every help would be appreciated. Maybe I did not understand the problem. I have the same trouble trying to merge BAM files...
Best regards, Anne