Question: How to install Picard/Pilons software and do variant call on a set of .sam files?
0
gravatar for elvissober
4.1 years ago by
elvissober20
South Africa
elvissober20 wrote:

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.

sequencing wgs software error • 1.5k views
ADD COMMENTlink modified 3.6 years ago by smkopac10 • written 4.1 years ago by elvissober20
1

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."

ADD REPLYlink written 3.6 years ago by smkopac10

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

ADD REPLYlink written 3.6 years ago by genomax76k
1
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

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.

ADD COMMENTlink modified 5 weeks ago by RamRS25k • written 4.1 years ago by Pierre Lindenbaum125k
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