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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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Running picard sam format converter for batch sample #53

Open zahraj242 opened 4 years ago

zahraj242 commented 4 years ago

Hello friends,

I have been using the following command for sam to bam conversion using picard; however, I do not know how to scale it up and do a batch conversion. Ideally, if I could ask picard to read all the sam files in a folder and convert them to bam files, that would be nice, if applicable. What would be the easiest way through? I would appreciate if you could guide me.

Best

Zara

java -jar picard.jar SamFormatConverter \

 I=test2.sam \

 O=results/test2.bam
zahraj242 commented 4 years ago

Solved writing a simple script in command line For i in {1..10}

Do

java -jar picard.jar SamFormatConverter \ I=$i.sam \ O=results/$i.bam Done :)