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Recent Replies
Comment: how to run FacetsSuite wrapper scripts on command line
by
GenoMax
129k
The [link in your original post][1] has this bit of help
--snp-pileup-path <path to snp-pileup executable>
So the path you provide ne…
Comment: ggsave() bug in ggplot2?
by
barslmn
★
1.5k
Can you run the command `file Figure1.jpg` and post the output?
Comment: PacBio Pipeline and Tools for Variant Call
by
Kiran
▴
70
Hi William , Thank you for the explanation, From VCF should i omit variants with `"/"` and keep ones with phased `"|"` for further annotati…
Comment: My kernel is killing the pairtools dedup script, how to prevent that?
by
GenoMax
129k
Keep an eye on memory usage. Even though you have 256G it is possible that the process is running out of memory or temp (/tmp) space. Try r…
Answer: Understanding Used Assembly: Why aren't authors specific about patch version?
by
GenoMax
129k
You may have seen explanation of the patches from GRC --> ([**LINK**][1]).
> The fact that patch-version does matter for looking up varian…
Comment: how to run FacetsSuite wrapper scripts on command line
by
Dalal
•
0
I apologise for that. Unfortunately I am still left with the same error:
> sh: 1: ~/mut_analysis/variant-calling/facets_cnv/:
> Permission…
Comment: BioInformatics, Software
by
barslmn
★
1.5k
https://bio.tools/ is a great website indexing software used in bioinformatics.
Comment: BioInformatics, Software
by
Pierre Lindenbaum
154k
This is just too broad. what did you find so far ?
Answer: How to calculate kinship matrix table from vcf file
by
barslmn
★
1.5k
You can use the vcftools relatedness2 module. Which implements the method describes in the paper: https://academic.oup.com/bioinformatics/a…
Answer: How to convert bed file to vcf?
by
Pierre Lindenbaum
154k
use AWK, change the header, body according to your needs...
awk 'BEGIN {printf("##fileformat=VCFv4.2\n##INFO=<ID=END,Number=1,Type=I…
Comment: Doubt - installing LncTar software
by
Jeremiah
•
0
It is the full result, there is only one lncRNA and one mRNA in Examp1, and the output file is just like web version reult
Comment: How to get a comperative result of 2 bed files?
by
Pierre Lindenbaum
154k
convert the bed to vcf and use truvari.
Comment: bioinformatic analysis protocol performed by CD Genomics
by
barslmn
★
1.5k
Mail their representative you talked with before or their support and ask them. There may not be a citable source. However, you can write t…
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