User: genomics Newbie

Reputation:
10
Status:
New User
Location:
Last seen:
2 weeks, 1 day ago
Joined:
9 months, 1 week ago
Email:
m*************@gmail.com

Posts by genomics Newbie

<prev • 29 results • page 1 of 3 • next >
2
votes
1
answer
121
views
1
answer
vcf filter of lowQual
... How do I filter my vcf so that all "lowQual" entries are excluded from the variant file. When I ran the following command I included the -e flag which I thought would exclude all LowQual, but they appear in my vcf and I need to remove them so that I can use my vcf as further input into another pi ...
vcf filter written 17 days ago by genomics Newbie10 • updated 16 days ago by Kevin Blighe26k
0
votes
0
answers
114
views
0
answers
plink .bim file missing variant ID
... Hello, First I generated a pileup from my BAM sequences and converted the pileup to vcf. samtools mpileup -uf ucsc.hg19.fasta sample_rna-seq.bam | bcftools call -mv -Oz > calls.vcf.gz I then used PLINK to make the bed, bim and fam files. Although the format was correct, the Variant ID was mi ...
.bim plink snp written 20 days ago by genomics Newbie10
5
votes
1
answer
99
views
1
answer
(Closed) convert .bed (uscs) format to .bed (plink) format
... Hello. Is it possible to convert a .ucsc .bed format to a plink .bed format without routing it through a .vcf? ...
.bed formats written 4 weeks ago by genomics Newbie10 • updated 4 weeks ago by Devon Ryan82k
5
votes
1
answer
194
views
6 follow
1
answer
bam to vcf to .bed
... Is the following the correct process? I do not believe I can "convert" .bam to .bed directly. I am converting .bam to vcf using bcftools, and then using plink to prepare .bed and .fam files. bed to vcf using bcftools vcf to bed using plink bed + fam using plink Thank you. ...
vcf bed bam written 5 weeks ago by genomics Newbie10 • updated 5 weeks ago by finswimmer4.5k
0
votes
0
answers
149
views
0
answers
Comment: C: Merging individual .bed files?
... SNP genotype analysis ...
written 5 weeks ago by genomics Newbie10
1
vote
0
answers
149
views
0
answers
Merging individual .bed files?
... Hello, Our main goal is to create a single set of .bed/.bim/.fam files from our .bam formatted sequences. However I’m finding that merging, sorting and indexing these .bam files (appox. 100) via samtools is exceeding our processing and storage capabilities. 1). Is there any other means by whic ...
.bam .bed samtools .bamtobed written 5 weeks ago by genomics Newbie10
3
votes
1
answer
154
views
1
answer
bam file merge
... Hello. I have numerous bam files which I need to merge into a single bam file. How do I know whether I need to first index and sort the bam files? ...
merge bam written 7 weeks ago by genomics Newbie10 • updated 7 weeks ago by h.mon18k
0
votes
1
answer
159
views
1
answers
Comment: C: Viewers for examining haplotypes
... Thank you for your reply! I have changed my original post from "all chromosomes" to only a specific few. Also, I have tried HaploView without success and Broad no longer supports the package. I think the genome viewers (i.e. IGV and UCSC genome viewer) might be useful? ...
written 10 weeks ago by genomics Newbie10
0
votes
1
answer
159
views
1
answer
Viewers for examining haplotypes
... Hello, What are some of the best software packages and viewers to examine haplotypes for a few specified chromosomes? Would IGV be appropriate? Generally are the input formats raw sequence files or can they be vcf files? I am trying to correlate this with ancestry. ...
haplotype chromosomes written 10 weeks ago by genomics Newbie10
0
votes
1
answer
267
views
1
answer
Variant Control Format (VCF) TO Mutation Annotation Format (.MAF)
... Is there an application which will accept a vcf as an input file and automatically prepare a .maf (mutation annotation format) for its output? I tried Ensemble's VEP application but could not save it in .maf format. Is the best alternative mskcc/vcf2maf ? Responses are appreciated! ...
vcf maf written 3 months ago by genomics Newbie10 • updated 3 months ago by adam.maikai440

Latest awards to genomics Newbie

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: 911 users visited in the last hour