This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to install Picard/Pilons software and do variant call on a set of .sam files?

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.

software error sequencing wgs
• 2,869 views • link
updated by smkopac • smkopac • written by elvissober • elvissober

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."

• 1 views • link
written by smkopac • smkopac

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

• 1 views • link
written by GenoMax GenoMax

1 answer

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.

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this