User: Pierre Lindenbaum

... install a java runtime (like [openjdk][1] version >=8) and update your [PATH][2] if needed. [1]: https://openjdk.java.net/install/ [2]: https://opensource.com/article/17/6/set-path-linux ...

written 2 days ago by Pierre Lindenbaum ♦ 131k

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Answer: C: Bedtools fisher test error

... check you don't have any column with a blank character (space, crlf, ... ) near the word '282763074'. ...

written 3 days ago by Pierre Lindenbaum ♦ 131k

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Answer: A: Publicly Available RNA-Seq Datasets from Human Heart

... https://www.encodeproject.org/matrix ...

written 3 days ago by Pierre Lindenbaum ♦ 131k

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Answer: A: Merge vcf with bcftools error wrong reference

... if your vcfs have a dictionary ( lines in the header starting with `##contig=`) , you can use my tool http://lindenb.github.io/jvarkit/HowManyBamDict.html that will produce a tab delimted file with the path to the vcf and a checksum for the dictionary. You'll get a signature for each distinct dic ...

written 3 days ago by Pierre Lindenbaum ♦ 131k

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Comment: C: Merge vcf with bcftools error wrong reference

... why not removing file_5000.vcf.gz from list_files_to_merge ? ...

written 3 days ago by Pierre Lindenbaum ♦ 131k

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Answer: A: Somatic Structure Variation on exome-seq data - pipeline recommendations?

... > My question is - is there any GATK workflow available to perform such an analysis? WDL: https://github.com/broadinstitute/gatk-sv >> A structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data. ...

written 5 days ago by Pierre Lindenbaum ♦ 131k

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Comment: C: Samtools error -1

... > EOF marker is absent. The input is probably truncated something wrong happened in the command that generated the bam file (before sorting), for example, check you have enough space on your disk. furthermore, with modern version of samtools , you don't have to convert the SAM to BAM before sort ...

written 5 days ago by Pierre Lindenbaum ♦ 131k

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Comment: C: Join two files with a common column

... Hello glady! We believe that this post does not fit the main topic of this site. not related to bioinformatics 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 disagree please tell us why in a reply bel ...

written 6 days ago by Pierre Lindenbaum ♦ 131k

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Comment: C: Join two files with a common column

... you want [join][1]. [1]: https://linux.die.net/man/1/join ...

written 6 days ago by Pierre Lindenbaum ♦ 131k

Latest awards to Pierre Lindenbaum

Great Question 3 days ago, created a question with more than 5,000 views. For Exome Aggregation Consortium (ExAC) database ?

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Scholar 12 days ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Appreciated 16 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Scholar 17 days ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Good Answer 18 days ago, created an answer that was upvoted at least 5 times. For A: Choosing Random Set Of Seqs From Larger Set

Popular Question 22 days ago, created a question with more than 1,000 views. For Ngs And Recalibration

Epic Question 22 days ago, created a question with more than 10,000 views. For What Is The Sequencing 'Depth' ?

Scholar 23 days ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Appreciated 24 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

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

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Scholar 4 weeks ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Scholar 5 weeks ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Scholar 5 weeks ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Appreciated 5 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Variant Calling pipeline to be run parallel on multiple cores

Scholar 5 weeks ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

Scholar 6 weeks ago, created an answer that has been accepted. For A: Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4

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