User: tjbencomo

gravatar for tjbencomo
tjbencomo10
Reputation:
10
Status:
New User
Location:
Last seen:
2 days, 11 hours ago
Joined:
4 months, 3 weeks ago
Email:
t********@gmail.com

Posts by tjbencomo

<prev • 4 results • page 1 of 1 • next >
1
vote
1
answer
132
views
1
answers
Answer: A: Publicly Available WGS Samples for Panel of Normals?
... I ended up using the hg38 1000 Genomes PON from the Broad linked to by @RamRS. Although the PON was most likely generated from samples sequenced using different prep protocols, one of the GATK developers says on the [GATK forum](https://gatk.broadinstitute.org/hc/en-us/community/posts/360061543792-P ...
written 5 days ago by tjbencomo10
0
votes
1
answer
132
views
1
answers
Comment: C: Publicly Available WGS Samples for Panel of Normals?
... I forget to mention I plan to run Mutect2 with a PoN and gnomAD to filter for germline variants. Would it be correct to say VarScan2 does the same thing as Mutect2 with the gnomAD VCF - filter germline variants using gnomAD? ...
written 12 days ago by tjbencomo10
0
votes
1
answer
132
views
1
answers
Comment: C: Publicly Available WGS Samples for Panel of Normals?
... It was my understanding that the PoN should consist of samples that were sequenced in a similar way to my own samples. I guess using the 1000g PoN could seem reasonable (although the assumption there is that their prep kit/sequencer is similar to mine - probably not a bad although not optimal assump ...
written 12 days ago by tjbencomo10
3
votes
1
answer
132
views
1
answer
Publicly Available WGS Samples for Panel of Normals?
... I have 15 tumors that were sequenced using whole genome sequencing at 30x depth. I would like to identify somatic variants using Mutect2. Unfortunately we don't have any normal samples, so I would like to build a Panel of Normals to use with Mutect2 in tumor-only to identify somatic variants. I also ...
wgs snp sequencing written 12 days ago by tjbencomo10

Latest awards to tjbencomo

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1656 users visited in the last hour