User: kevin.stachelek

Reputation:
0
Status:
New User
Last seen:
1 week, 5 days ago
Joined:
3 years, 1 month ago
Email:
k**************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by kevin.stachelek

<prev • 4 results • page 1 of 1 • next >
0
votes
0
answers
112
views
0
answers
Comment: C: Double Check VCF Calls in Corresponding .bam Files
... I believe that any caller will only make a call at a site which differs from the reference, otherwise the file size of vcfs would be huge. Is it true that most would have built in filters for mapping quality and base quality, i.e. --min-MQ or --min-BQ for mpileup > bcftools. Just to be clear, i ...
written 16 days ago by kevin.stachelek0
0
votes
0
answers
112
views
0
answers
Double Check VCF Calls in Corresponding .bam Files
... I have a set of variant calls from GATK Mutect2 in matched tumor/normal samples that are found in a subset of my sequencing cohort. I'd like to determine the allele frequency at each site in every sample, to determine whether these variants are being mistakenly filtered in some samples. I could just ...
sequencing written 17 days ago by kevin.stachelek0
0
votes
2
answers
4.9k
views
2
answers
Comment: A: Where can I get ?or how can I make a mappability track for hg38 assembly
... If you are working with UCSC hg19 there are pre-built mappability files from ENCODE available [here][1]. [1]: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/ ...
written 3 months ago by kevin.stachelek0
0
votes
0
answers
199
views
0
answers
Plot pileup of reads multiply aligned to repetitive elements
... I am looking at repetitive elements as a biomarker in cancer. We have identified a few candidate repetitive elements via [tetranscripts][1]. I've taken a couple of approaches to visualizing this data: 1. bedtools using a reference bed file from repbase/UCSC browser then a simple barplot of overla ...
bedtools plotting repmasker written 7 months ago by kevin.stachelek0

Latest awards to kevin.stachelek

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: 2115 users visited in the last hour