User: badredda

gravatar for badredda
badredda30
Reputation:
30
Status:
New User
Location:
Last seen:
1 month ago
Joined:
6 months, 2 weeks ago
Email:
b*******@igbmc.fr

Posts by badredda

<prev • 7 results • page 1 of 1 • next >
1
vote
1
answer
178
views
1
answers
Comment: C: [solved] SnpEff reports intron variants in exons ?
... @Kevin Blighe Thank you for the explanation. I will take your opinion into consideration next time. @fin swimmer Thank you for your help. Actually, that variant coming in the blue bar of GRCh37.75 was an intron. I am laughing at myself now for misunderstanding :)) Everything's cleared. Thanks again ...
written 6 weeks ago by badredda30
0
votes
1
answer
178
views
1
answers
Comment: C: SnpEff reports intron variants in exons ?
... Now I am a bit confused. I expected it to be exonic because the variant comes within the exon as shown in IGV when its being annotated with GRCh37.75. I followed your link to ensembl and indeed it does show it being an intron or downstream intron. Is it me misinterpreting the representation of the g ...
written 6 weeks ago by badredda30
0
votes
1
answer
178
views
1
answers
Comment: C: SnpEff reports intron variants in exons ?
... Hello finswimmer, yes, here's the line of the variant shown above in the IGV for GRCh37.75: chr1 1573078 rs201088964 A G . alt_allele_in_normal;panel_of_normals DB;ECNT=1;HCNT=12;MAX_ED=.;MIN_ED=.;NLOD=7.46;TLOD=8.02;ANN=G|downstream_gene_variant|MODIFIER|MMP23B|ENSG00000189409|transcript|ENST ...
written 6 weeks ago by badredda30
4
votes
1
answer
178
views
1
answer
[solved] SnpEff reports intron variants in exons ?
... Dear community, I am working on produced VCF files from whole exome sequencing prostate cancer patients using MuTect2. I have compared normal/tumor matched samples and found mutations. During library preparation, we used a kit for exome capture (SureSelect Human All Exon V6). Next, I wanted to perf ...
annotation snpeff exome-seq snp written 6 weeks ago by badredda30 • updated 6 weeks ago by cpad01122.9k
0
votes
0
answers
116
views
0
answers
CHASM vs VEST
... Hello dear Biostars community, I would like to use CRAVAT(https://www.cravat.us/) tools VEST and CHASM for somatic functional annotation but I can't figure out the difference between the two tools. Both of the tools uses a machine learning method and I know that VEST include also indels (which CHAS ...
chasm vest cravat functional somatic annotation written 10 weeks ago by badredda30
0
votes
1
answer
297
views
1
answers
Comment: C: Intersection of a BED genes with multiple VCFs: report only if at least N inters
... @Alex Reynolds Thanks for the help ! I will try it asap ! ...
written 6 months ago by badredda30
4
votes
1
answer
297
views
1
answer
Intersection of a BED genes with multiple VCFs: report only if at least N intersection.
... Hello everyone, Here's my problem: I have multiple VCF outputs that I have obtained using MuTect2 for 18 patients in total from Whole Exome Sequencing (WES/WXS) (so 18 VCF files). I have a BED file which has the list of all genes. FYI, MuTect2 reports single variants and INDELS in the VCF. So, if ...
bedtools vcf wes bed intersection written 6 months ago by badredda30 • updated 6 months ago by Alex Reynolds21k

Latest awards to badredda

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: 1033 users visited in the last hour