Admin: Pierre Lindenbaum
Pierre Lindenbaum ♦ 115k
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Posts by Pierre Lindenbaum
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Hello p.hadjipanayiotou!
Questions similar to yours can already be found at:
Survey - Tell me about your Bioinformatics struggles
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. ...
written 5 hours ago by
Pierre Lindenbaum ♦ 115k
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... answering questions about omics data analysis. ...
written 5 hours ago by
Pierre Lindenbaum ♦ 115k
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Comment:
C: Biostar Bioinformatics textbooks
... Hello Charles Olweny !
We believe that this post does not fit the main topic of this site.
post should be written in the biostars handbook thread
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you disagre ...
written 7 hours ago by
Pierre Lindenbaum ♦ 115k
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... > but it's a little tricky considering I can't align the forward reads.
so R1 won't be mapped but R2 will. And then filter with samtools ...
written 18 hours ago by
Pierre Lindenbaum ♦ 115k
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... see https://www.biostars.org/p/276858/ ...
written 19 hours ago by
Pierre Lindenbaum ♦ 115k
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... GATK SelectVariants https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php
with
```
--concordance Freebayes.vcf
```
> A site is considered concordant if (1) we are not looking for specific samples and the ...
written 22 hours ago by
Pierre Lindenbaum ♦ 115k
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Comment:
C: R package openxlsx and gradient
... how is it related to bioinformatics ? ...
written 1 day ago by
Pierre Lindenbaum ♦ 115k
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... using **vcffilterjdk** http://lindenb.github.io/jvarkit/VcfFilterJdk.html
an example with 3 populations
select.code:
final String POP1[]={"S1"};
final String POP2[]={"S2","S3"};
final String POP3[]={"S4","S5"};
final String ALL_POPS[][]={POP1,POP2,POP3};
for(String p ...
written 1 day ago by
Pierre Lindenbaum ♦ 115k
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... > This however, seems very time intensive and computationally cumbersome. What would be the alternatives to this ?
GATK hapcaller in **gvcf** mode: https://software.broadinstitute.org/gatk/documentation/article.php?id=3893
![enter image description here][1]
[1]: https://us.v-cdn.net/501979 ...
written 2 days ago by
Pierre Lindenbaum ♦ 115k
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... > As for your second point, I am not really sure what you suggest. Do you mean I should provide one chromosome at a time and run the job in parallel?
yes ...
written 2 days ago by
Pierre Lindenbaum ♦ 115k
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