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Recent Replies
Comment: how to run FacetsSuite wrapper scripts on command line
by
Dalal
•
0
This is the code I ran:
Rscript --vanilla snp-pileup-wrapper.R --snp-pileup-path ~/mut_analysis/variant-calling/facets_cnv/ --vcf-file ~/mu…
Answer: Michigan Imputation Server - Local docker image
by
Vincent Laufer
★
2.8k
Hi Ms. or Mr. Effect,
A couple ideas:
1) if its not working on the local docker image, have you tried uploading your data for imputat…
Answer: Manhattan Plot with independent significant hits
by
Vincent Laufer
★
2.8k
Consider using [locuszoom][1] for genomic regions small enough to warrant special clarification that the two associations are independent.
…
Comment: Problem with PGDSpider v 2.1.0.2
by
sackettl
▴
20
I have this same problem with version 2.1.1.5. Did you ever find a solution?
Comment: Filter VCF file for variant alleles
by
Ram
39k
> can't find anything to do this
It's in there. If you had looked a little deeper, you would have found - on your own - exactly what Pierr…
Comment: To call variants can I use my aligned WGS data as a reference genome
by
GenoMax
129k
Then create an alternate Reference with data for the sample: https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateR…
Comment: Help making ADMIXTURE output digestible
by
Aaron
▴
10
You can also check out [pong][1] (README [here][2]), which creates interactive plots with the clusters and colors automatically aligned acr…
Comment: To call variants can I use my aligned WGS data as a reference genome
by
mls
•
0
Yes they are but I wanna compare one of my samples with others , rather S288C.
Comment: To call variants can I use my aligned WGS data as a reference genome
by
Pierre Lindenbaum
154k
the bam are mapped on S288C fasta isn't it ? why would you need another reference ?
Comment: Filter VCF file for variant alleles
by
Pierre Lindenbaum
154k
use a filtering expression https://samtools.github.io/bcftools/bcftools.html#expressions , something like;
bcftools view -i 'COUNT(GT=…
Comment: Filter VCF file for variant alleles
by
miguellarrazlopezdenovales
•
0
I've tried bcftools, which seems to be the closest I've got, but I can't find anything to do this. I have also found vcftools --max-non-ref…
Comment: Filter VCF file for variant alleles
by
Ram
39k
What have you tried? You've mentioned bcftools as a tag, have you read the manual?
Comment: How to concatenate multiple fasta file
by
doggie
•
0
@shenwei356 Thank you so much! Your prompt reply helped me a lot!
Answer: PacBio Pipeline and Tools for Variant Call
by
William Rowell
▴
250
> What are Quality parameters that should be taken care ( Adapter trim, Reads filter, Min Data size, ) How to trim adapter, What tools to u…
Comment: Ambient RNA expression correction
by
rpolicastro
12k
Ambient RNA would have the same cell barcode as a valid cell-containing droplet since the RNA gets partitioned into the droplet with the ce…
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