How to install Picard/Pilons software and do variant call on a set of .sam files?

Question

[elvissober]

How to install Picard software and do variant call on a set of .sam files? I have unzipped the archive, read the docs, not clear how to run it from a folder and what commands call variants on .sam and .bam files. Thank you.

[smkopac]

I am also having trouble running Pilon. When I use the command above to get help for the.jar file, I get an error saying "No main manifest attribute."

[GenoMax]

Please post the command you are trying to use that is giving you an error.

Answer 1

[Pierre Lindenbaum]

get help:

java -jar /path/to/picard.jar

get help for specific sub-program

java -jar /path/to/picard.jar MergSamFiles

run a specific sub-program

java -jar /path/to/picard.jar MergSamFiles I=f1.bam I=f2.bam O=o.bam

or

find ./ -name "*.bam" > in.list
java -jar /path/to/picard.jar MergSamFiles I=in.list O=o.bam

there is nothing in picard for calling variants. See gatk or samtools.