User: William

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William4.5k
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Posts by William

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How to remove duplicate reads / create consensus reads based on umi tags in 2nd fastq file?
... In a targeted sequencing dataset, I have for each sample a `r1.fastq.gz` file and a `umi.fastq.gz` file. How can I use the short umi tags that are in the `umi.fastq.gz` file, to remove duplicates or create a consensus sequence of the reads in the `r1.fastq.gz` file? Or do I need to go back to, o ...
umi written 6 weeks ago by William4.5k
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Comment: C: Difference between . and ./. for missing genotype in VCF
... The single record is from the output of a recent variant calling of a diploid organism with GATK4. GATK4 variant called multiple samples via GenotypeGVCFs (i.e. there was intermediate GVCF output that was later merged). ...
written 15 months ago by William4.5k
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Difference between . and ./. for missing genotype in VCF
... What is the difference between . and ./. for a missing genotype in a VCF file? For example in one VCF record I have these two sample genotypes. GT:AD:DP:GQ:MMQ:PGT:PID:PL .:0,0:.:.:.:.:.:. ./.:0,0:0:.:.:.:.:0,0,0 There is also is a difference in which genotype attributes are 0 or . ...
vcf written 15 months ago by William4.5k • updated 15 months ago by Santosh Anand5.0k
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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 23 months ago by William4.5k
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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 23 months ago by William4.5k
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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 23 months ago by William4.5k
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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 23 months ago by William4.5k
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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 23 months ago by William4.5k
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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 23 months ago by William4.5k
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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 23 months ago by William4.5k • updated 23 months ago by Sean Davis25k

Latest awards to William

Appreciated 16 days ago, created a post with more than 5 votes. For A: Best Genome Browser To Look At Structural Variation Calls
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Best Genome Browser To Look At Structural Variation Calls
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Best Genome Browser To Look At Structural Variation Calls
Popular Question 4 months ago, created a question with more than 1,000 views. For Google Genomics and Broad Institute Team Up to Tackle Genomic Data
Great Question 4 months ago, created a question with more than 5,000 views. For Bio-informatics salary distribution versus Java salary distribution in the UK
Teacher 10 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?
Popular Question 10 months ago, created a question with more than 1,000 views. For Best tool to create a graphical (QC) summary report based on a VCF file?
Great Question 10 months ago, created a question with more than 5,000 views. For Bio-informatics salary distribution versus Java salary distribution in the UK
Popular Question 10 months ago, created a question with more than 1,000 views. For Which Illumina data to generate for constructing benchmark SNP / SV genotypes
Popular Question 10 months ago, created a question with more than 1,000 views. For Output per variant and per sample heterozygosity fraction from VCF.
Popular Question 10 months ago, created a question with more than 1,000 views. For Google Genomics and Broad Institute Team Up to Tackle Genomic Data
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Combining Data Of Multiple Vcfs Into One.
Appreciated 10 months ago, created a post with more than 5 votes. For A: Best Genome Browser To Look At Structural Variation Calls

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