Admin: Pierre Lindenbaum

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France/Nantes/Institut du Thorax - INSERM UMR1087
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Posts by Pierre Lindenbaum

<prev • 9,323 results • page 1 of 933 • next >
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Answer: A: Is it possible to pipelined two picard tools into one input?
... try java -jar picard.jar CleanSam \ I=abc.bam \ O=/dev/stdout |\ java -jar picard.jar SamToFastq \ I=/dev/stdin \ FASTQ=R1.fastq \ SECOND_END_FASTQ=R2.fastq ...
written 7 hours ago by Pierre Lindenbaum129k
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Comment: C: How do I get repeating regions from fasta file or directly from internet
... http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/simpleRepeat.txt.gz ? ...
written 15 hours ago by Pierre Lindenbaum129k
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Answer: C: How to extract sample IDs from VCF into new VCF?
... > I've written a script that extracts VCF IDs from a large VCF, in order to get a subset of the sample IDs (people). isn't it a job for `bcftools view --samples ` ? ...
written 1 day ago by Pierre Lindenbaum129k
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Comment: C: vcf of SV (structural variant): how to retrieve/separate Germline and Somatic SV
... https://www.biostars.org/p/224702/ https://www.biostars.org/p/78929/#115693 https://www.biostars.org/p/12535/#115691 ...
written 1 day ago by Pierre Lindenbaum129k
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Answer: A: Extracting Snps with pvalue <5x10-8 from gwas result
... with the example your provided above, the following awk script works: awk '($4<1E-1) {print $1}' input.txt furthermore: check your LOCALE : https://www.gnu.org/software/gawk/manual/html_node/Locale-influences-conversions.html ...
written 1 day ago by Pierre Lindenbaum129k
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Comment: C: Extracting Snps with pvalue <5x10-8 from gwas result
... what does the input look like ? show us a few lines. ...
written 1 day ago by Pierre Lindenbaum129k
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Comment: C: Want to create a new Index file for BAM using SAMTOOLS. Do I need to sort the de
... From the 1st screenshot, I suspect you're using the wrong fasta reference . ![enter image description here][1] Furthermore, the command `samtools view -H your.bam | head` should show you if the sort-order is `coordinate` [1]: https://img.techpowerup.org/200707/3.jpg ...
written 2 days ago by Pierre Lindenbaum129k
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Answer: A: igvtools count | wigToBigWig, pipe not working for some reason although stdout a
... try: igvtools count -w 10 -f median $file stdout hg19 | grep -v "Using system JDK" | wigToBigWig stdin hg19.chrom.sizes ${name}.bw another option: edit the script igvtools try to replace https://github.com/igvteam/igv/blob/6960eaf1b04d5932429060bd6ff4b0f053c4be1e/scripts/igvtools#L10 ec ...
written 2 days ago by Pierre Lindenbaum129k
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Comment: C: How to merge 2 VCF files that was previously extracted from same file
... > at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:226) There cannot be an error at line 226 in MergeVcfs https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/vcf/MergeVcfs.java#L226 . Please, update your version of picard. ...
written 2 days ago by Pierre Lindenbaum129k
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Comment: C: How to retrive sequnce from fasta file by using start and end point data from xl
... duplicate: https://www.biostars.org/p/144155/ ; https://www.biostars.org/p/128224/ ; https://www.biostars.org/p/169469/ ; ... etc... etc... ...
written 3 days ago by Pierre Lindenbaum129k

Latest awards to Pierre Lindenbaum

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Scholar 4 days ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Scholar 4 days ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Appreciated 5 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 7 days ago, created an answer that has been accepted. For A: bcftools view VCF parse error
Scholar 9 days ago, created an answer that has been accepted. For A: quality check of bam files
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Scholar 16 days ago, created an answer that has been accepted. For A: quality check of bam files
Appreciated 18 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Popular Question 20 days ago, created a question with more than 1,000 views. For Ngs And Recalibration
Scholar 20 days ago, created an answer that has been accepted. For A: quality check of bam files
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Appreciated 27 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 27 days ago, created an answer that has been accepted. For A: quality check of bam files
Scholar 27 days ago, created an answer that has been accepted. For A: quality check of bam files
Scholar 29 days ago, created an answer that has been accepted. For A: quality check of bam files
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Choosing Random Set Of Seqs From Larger Set
Great Question 4 weeks ago, created a question with more than 5,000 views. For Exome Aggregation Consortium (ExAC) database ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Choosing Random Set Of Seqs From Larger Set
Appreciated 5 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Choosing Random Set Of Seqs From Larger Set
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Scholar 6 weeks ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header

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