User: William

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William3.9k
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Posts by William

<prev • 296 results • page 1 of 30 • next >
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How to do a local denovo assembly including unmapped paired reads for many samples to genotype a large insertion.
... I have a set of many bam files for which I would like to know if an insertion of a few 100bp is present at a certain locus. The insertion variant is not picked up by small variant callers like freebayes, gatk or structural variant callers like lumpy or manta when doing a full genome variant callin ...
local assembly written 7 weeks ago by William3.9k • updated 7 weeks ago by h.mon9.0k
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Comment: C: Is it possible to use haplotypes instead of SNPs for association testing with ph
... Thank you for the haplotype association link. I'll look in to the tools / papers listed there. I added a reference for what I mean with genomic selection as a comment to the orginal question. ...
written 10 weeks ago by William3.9k
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Comment: C: Is it possible to use haplotypes instead of SNPs for association testing with ph
... Reference for genomic selection method http://www.genetics.org/content/157/4/1819 ...
written 10 weeks ago by William3.9k
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Is it possible to use haplotypes instead of SNPs for association testing with phenotypes?
... > We need to start thinking about genome analysis as haplotype reconstruction- not variant calling https://twitter.com/deannachurch/status/877192436459745280 Using new technology like linked reads or long reads it is becoming much easier to identify haplotypes in genomes, ie. collections of phas ...
haplotypes gwas snp written 10 weeks ago by William3.9k • updated 10 weeks ago by GabrielMontenegro330
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Comment: C: Python library for parsing bcftools stats file
... pyvcf is parsing VCF files, I am looking for a parser for VCF/BCF **stats** files generated by **bcftools stats**. ...
written 11 weeks ago by William3.9k
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Python library for parsing bcftools stats file
... Did someone already create a python library for parsing bcftools stats output files? BCFTools stats generates a txt stats file from VCF/BCF files. These text stats files contains some tab delimited tables and key value pairs that I would like to acces programmatically in python. Depending on the ...
bcftools written 11 weeks ago by William3.9k
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Answer: A: How to determine percentage missing genotypes in VCF/BCF?
... I always prefer not having to write custom code, but this is short and will do the trick: from cyvcf2 import VCF reader = VCF("my.vcf.gz") num_var = 0 num_called = 0 for variant in reader: num_var += 1 num_called += variant.num_called num_called / (num_var ...
written 3 months ago by William3.9k
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How to determine percentage missing genotypes in VCF/BCF?
... Is there a command line tool that has a quick function to determine the percentage of missing genotypes in a VCF/BCF file? Or the inverse of the missing percentage, the genotype occupancy % of the VCF/BCF file? Preferable a tool where I don't need to accumulate the missingness per sample of per va ...
vcf written 3 months ago by William3.9k
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Can IonProton sequencing data be processed using BWA + FreeBayes or CLC?
... Iontorrent data used to have big homopolymer issues, the sequencing machine did output some Iontorrent specific quality information that only Iontorrent specific aligners and variant calling software could use. The homopolymer issue seems to have been improved with the IonProton machine, but it's ...
ionproton written 4 months ago by William3.9k
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Answer: A: GBS and RADseq
... As umbrella terms GBS and RadSeq mean the same thing. A sequencing protocol where restriction enzymes and DNA restriction sites are involved. See also this RadSeq/GBS Nature Genetics Review from beginning of 2016. It has some nice tables of all different GBS/RadSeq methods: http://www.nature.com/ ...
written 5 months ago by William3.9k

Latest awards to William

Student 15 days ago, asked a question with at least 3 up-votes. For Difference Between Somatic And Germline Variant Calling?
Student 3 months ago, asked a question with at least 3 up-votes. For Recent Review / Best practices for (meta) micro array expression data analysis
Popular Question 4 months ago, created a question with more than 1,000 views. For Best Fastq Quality Overview Tool
Good Question 5 months ago, asked a question that was upvoted at least 5 times. For Best Genome Browser To Look At Structural Variation Calls
Teacher 5 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?
Great Question 6 months ago, created a question with more than 5,000 views. For Difference Between Somatic And Germline Variant Calling?
Great Question 6 months ago, created a question with more than 5,000 views. For Difference Between Somatic And Germline Variant Calling?

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