Admin: Pierre Lindenbaum
Pierre Lindenbaum ♦ 106k
- Reputation:
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- France/Nantes/Institut du Thorax - INSERM UMR1087
- Website:
- http://plindenbaum.blo...
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- 8 years, 2 months ago
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Posts by Pierre Lindenbaum
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... **I'm sure this solution works** but, in the general case:
allele = gt.split("/")
doesn't work if the genotype is phased.
int(data[1])+len(data[3])-2,
doesn't work if there is a `INFO/END`
if allele[0] == allele[1]:
doesn't work if genotype is nocall `./.` or not diallelic ...
written 11 hours ago by
Pierre Lindenbaum ♦ 106k
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Comment:
C: install of STAR
... Hello yueli7!
We believe that this post does not fit the main topic of this site.
just a PATH problem https://opensource.com/article/17/6/set-path-linux "Telling your Linux shell where to look for executable files is easy, and something everyone should be able to do."
For this reason we have clo ...
written 12 hours ago by
Pierre Lindenbaum ♦ 106k
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... using bioalcidaejdk: http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html
$ java -jar dist/bioalcidaejdk.jar -e 'stream().forEach(V->println(V.getContig()+" "+V.getStart()+" "+V.getEnd()+" "+V.getGenotype(0).getAlleles().stream().map(A->A.isCalled()?A.getDisplayString():".").collect(Collec ...
written 12 hours ago by
Pierre Lindenbaum ♦ 106k
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Comment:
C: Merging two fastq.gz files
... not need to use `gzcat`, just use `cat` https://www.biostars.org/p/136025/ ...
written 14 hours ago by
Pierre Lindenbaum ♦ 106k
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... https://www.rcsb.org/pdb/static.do?p=download/web_download/download.jsp ?? ...
written 17 hours ago by
Pierre Lindenbaum ♦ 106k
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... what have you tried ? ...
written 18 hours ago by
Pierre Lindenbaum ♦ 106k
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... how did you get call vcf from the bam ? bcftools ? gatk ? ...
written 21 hours ago by
Pierre Lindenbaum ♦ 106k
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... search a **program group** in the bam header for gatk IndelRealigner
e.g:https://github.com/samtools/samtools/blob/9df632114a537f57928e4b2c17fbb1928679f877/test/dat/mpileup.1.sam
@PG ID:bam_realignment_around_known_indels.1 PN:GenomeAnalysisTK PP:gatk_target_interval_creator.1 VN:1.2-29-g0acaf ...
written 1 day ago by
Pierre Lindenbaum ♦ 106k
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... I don't know if it's going to work with javac 10, but try to add the source and target flags in
https://github.com/lindenb/jvarkit/blob/master/Makefile#L885
${JAVAC} -source 1.8 -target 1.8 -d ${tmp.dir} (....)
and
https://github.com/lindenb/jvarkit/blob/master/Makefile#L106
${JAVAC} ...
written 1 day ago by
Pierre Lindenbaum ♦ 106k
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... this question has been asked a large number of times here. Please search for this question. Nevertheless, regarding your code, instead of doing your loop liste-nth times. How about scanning the fasta only one time and check if the current fasta name is in your `liste` ? ...
written 1 day ago by
Pierre Lindenbaum ♦ 106k
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