Our documentation websites are currently offline due to a data center fire. We do not yet have an ETA for restoring service; we’ll update this message when we know more.
- Last Active
- Member, Broadie, Moderator
Hi @sergey_ko13, The two files are different. The altalt.sam file is the input to k8 bwa-postalt processing. The output is altalt_postalt.sam: k8 bwa-postalt.js \ chr19_chr19_KI270866v1_alt… (View Post)
Hi @CompBio1234567, It appears you are using a CHAIN file that expects hg19 nomenclature, e.g. chr22. (Quote) You can double-check this by looking into the CHAIN file. Your input VCF shows G… (View Post)
Hi @FPBarthel, Thanks for pointing out the broken link. Looks like some folks reorganized that section of the repo and the linked document was deleted in the process. The broken link is https:/… (View Post)
Hi @stefstef, The quick answer is no. gCNV coverage collection is the same as for the somatic workflow. In terms of qualities, CollectReadCounts only takes into consideration mapping quality. The … (View Post)