- Last Active
@Sheila Thanks for your reply.I know MarkDuplicates can largely control false positives.I just can't believe its runtime though set -Xmx#G and TMP_DIR even -XX:ParallelGCThreads to add threads.Is it because the numerous duplicate reads of my data?…
Also in Indel realignment, should I use somatic indel database VCF as knownSites?
Thanks for your reply.I believe the user as you said also manipulated the file by removing the blank spaces in the INFO column of hapmap vcf. You can compare the following two files: before removing: after removing: I don't know why the downl…
Thank you for your reply. I downloaded the Hapmap VCF from http://www.broadinstitute.org/cancer/cga/contest_download and it actually worked when using old version ContEst also downloaded from CGA website.I think it's the difference of handling the p…