User: William

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William4.2k
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Posts by William

<prev • 312 results • page 1 of 32 • next >
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Answer: A: find homozygous SNPs between two samples's VCF files.
... This can be done 2 two bcftools commands piped together. The first command selects the two samples of interest out of a VCF that can have multiple samples The second commands filters on that 4 alleles have to be called in total, of which 2 alternative and excludes variants were any of the two samp ...
written 8 weeks ago by William4.2k
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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
... I was looking for something R specific Pierre. VcfFilterJdk is as R specific as writing an CYVCF2 python script and then executing that via R system2 call to the CYVCF2 script. ...
written 9 weeks ago by William4.2k
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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
... Just load a TAB file as a data frame is certainly an option. I was hoping there would be a R library that would support: - working on larger genotype tabels than can be loaded as a data-frame - be more user friendly, i.e. offer pre-defined domain specific filters like for example bcftools does (i ...
written 9 weeks ago by William4.2k
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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
... the VCF can optionally be converted to TAB delimited format with bcftools query. Or to any specific R format. ...
written 9 weeks ago by William4.2k
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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
... Sometimes the input VCF already has been filtered for regions and samples of interest. So it's now always very big (i.e. could be opened in Excel if you really wanted to) , but sometimes it still is very big (more suited for streaming processing with bcftools/cyvcf2). ...
written 9 weeks ago by William4.2k
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Comment: C: How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using
... Targeted downstream users are R(studio) users who would like to have this functionality in the environment that they are used to and already use for related tasks. ...
written 9 weeks ago by William4.2k
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How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using BCFTools,CYVCF2 or Excel
... How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using BCFTools,CYVCF2 (fast python VCF/BCF parser) or Excel? Support for at least the following type of filter criteria is required: - Filtering on Region of Interest - Filtering on Samples of interest - Filtering on Var ...
vcf R snp filtering written 9 weeks ago by William4.2k • updated 9 weeks ago by Sean Davis24k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... Why is BBMAP more close to the sensitivity of BLAST than the other short read aligners like BWA/SNAP/minimap2? And is it still fast (since it is written in Java?)? ...
written 3 months ago by William4.2k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... Why is hisat2 more close to the sensitivity of BLAST than the other short read aligners like BWA/SNAP/minimap2? Is it because of the multiple index types? ...
written 3 months ago by William4.2k
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Comment: C: Sensitive (BLAST like) and fast alignment of millions of sequences against human
... Correct, I am aligning DNA fragments of ca 200 bp against indexed genomes (DNA) of human size and smaller. ...
written 3 months ago by William4.2k

Latest awards to William

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Where/How To Assess Which Bioinformatics Tools/Databases Are Most Used/Accessed?
Student 7 months ago, asked a question with at least 3 up-votes. For Difference Between Somatic And Germline Variant Calling?
Student 7 months ago, asked a question with at least 3 up-votes. For Difference Between Somatic And Germline Variant Calling?
Student 10 months ago, asked a question with at least 3 up-votes. For Recent Review / Best practices for (meta) micro array expression data analysis

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