sorting bam file using Picard tools

Question

[anithabioinfor]

Unable to access jarfile picard-tools/SortSam.jar i am getting error like this can anybody help me to rectify this for SNP and indels calling

[WouterDeCoster]

The path is incorrect or the file does not exist. Check where SortSam.jar is.

Answer 1

[Pierre Lindenbaum]

your manual/doc is old there is no such SortSam.jar , the modern command should look like

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

[BENYEBUGA]

I'm getting a similar error "Error: Unable to access jarfile /home/ben/jar_files/picard.jar" using this command:

 java -jar /home/ben/jar_files/picard.jar ReorderSam \
                  INPUT=I19139.hg19.bam \
                  OUTPUT=reordered.bam \
                  REFERENCE=hg19.fa

Path: \wsl$\Ubuntu\home\ben\jar_files

Any ideas? I've installed the latest version of java-default as of today.