Admin: Pierre Lindenbaum
Pierre Lindenbaum ♦ 108k
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Posts by Pierre Lindenbaum
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1
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... see https://www.biostars.org/p/15992/ ; ...
written 12 hours ago by
Pierre Lindenbaum ♦ 108k
4
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49
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Answer:
A: Issue with Bcftools reheader
... the option -s of bcftools reheader is a **FILE** not a string. https://samtools.github.io/bcftools/bcftools.html
-s, --samples FILE
new sample names, one name per line, in the same order as they appear in the VCF file. Alternatively, only samples which need to be renamed can be listed ...
written 17 hours ago by
Pierre Lindenbaum ♦ 108k
0
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1
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92
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1
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... If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
![Upvote|Bookmark|Accept][1]
[1]: http://i68.tinypic.com/2m2ykjr.png
...
written 19 hours ago by
Pierre Lindenbaum ♦ 108k
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2
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66
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Comment:
C: GATK3 error message
... > your data is corrupted
try to understand what I've done in my previous comment please https://www.biostars.org/p/321787/#321805 ...
written 21 hours ago by
Pierre Lindenbaum ♦ 108k
0
votes
2
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66
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Comment:
C: GATK3 error message
... there is no problem with that resource. *your* data is corrupted.
$ curl "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Homo_sapiens_assembly38.fasta.gz" | gunzip -c | grep -v '^>' | tr -d '[ATGCNatgcn\n]' | grep -o '.' | sort | uniq -c
2 B
8 K
...
written 22 hours ago by
Pierre Lindenbaum ♦ 108k
0
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2
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66
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2
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Comment:
C: GATK3 error message
... what devon said:
> your fasta file is likely corrupted, since it has a \ in it as a base.
futhermore there is a 'O'.
I also suggest you have a look at this fasta file:
grep -n -A 5 -B 5 '/' ref.fasta ...
written 22 hours ago by
Pierre Lindenbaum ♦ 108k
0
votes
2
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66
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2
answers
Answer:
C: GATK3 error message
... what is the version of gatk ?
what is the output of:
grep -v '^>' /path/to/Homo_sapiens_assembly38.fasta | tr -d '[ATGCNatgcn\n]' | grep -o '.' | sort | uniq -c ...
written 23 hours ago by
Pierre Lindenbaum ♦ 108k
0
votes
2
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117
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2
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Comment:
C: Programming interview via Skype
... How to have technical and coding interviews over Skype https://blogs.skype.com/tips/2017/08/25/how-to-have-technical-and-coding-interviews-over-skype/?eu=true ...
written 1 day ago by
Pierre Lindenbaum ♦ 108k
0
votes
0
answers
53
views
0
answers
... see https://www.biostars.org/p/221662/ ...
written 1 day ago by
Pierre Lindenbaum ♦ 108k
0
votes
2
answers
168
views
2
answers
... from twitter:
https://twitter.com/m_foll/status/1009165148391661570 ...
written 1 day ago by
Pierre Lindenbaum ♦ 108k
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