Moderator: Kevin Blighe

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Kevin Blighe11k
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London/Brazil
Website:
https://github.com/kev...
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35 minutes ago
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4 months, 2 weeks ago
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Mostly unavailable from January 12 to January 22

Posts by Kevin Blighe

<prev • 1,608 results • page 2 of 161 • next >
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Comment: C: MAF file handling
... No, this relates to the Mutation Annotation Format files that are listed in the TCGA - it does not relate to **m**inor **a**llele **f**requency. One issue with using this open-access mutation data from the TCGA is that different tools were used to call these variants that are listed in each MAF fil ...
written 4 days ago by Kevin Blighe11k
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Answer: A: help with format of hapotype snp files
... I would encourage you to transform everything into a PLINK dataset and then merge them within PLINK. For conversion of HAPS to PLINK format, take a look here: - https://www.biostars.org/p/17266/ - File format reference - haps (Oxford phased haplotype file) If you have data in VCF or BCF, and ...
written 4 days ago by Kevin Blighe11k
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Comment: C: Row-specific findOverlaps of two GRanges datasets
... It would help to paste some sample data and to show the result that you want. ...
written 4 days ago by Kevin Blighe11k
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Comment: C: Quick help: How can I find and replace a specific nucleotide within a gene seque
... I have tidied it a fair bit to how [I believe..] it should look ...
written 4 days ago by Kevin Blighe11k
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Comment: C: Compare genotypes between WGS and Targeted pannel
... Would Spanish be considered Caucasian or Hispanic? The idea of merging with 1000 Genomes is to specifically gauge the influence of ethnicity in your cohort. Without correcting for ethnicity, you may make false-associations. You should, in that case, merge your 2 datasets together, and then merge wi ...
written 4 days ago by Kevin Blighe11k
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Comment: C: Annovar Region Annotation
... Paste the commands that you have been using, and also the commands that you used to install the databases. ...
written 5 days ago by Kevin Blighe11k
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Answer: A: Access array in bcftools
... Provided the formatting is consistent all the way through the VCF or BCF, I would avoid tools like bcftools for filtering and just use AWK: Here is an example: cat test.vcf ##fileformat=VCFv4.0 ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal tumour ch ...
written 6 days ago by Kevin Blighe11k
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Comment: C: gene id identification
... For OP: I did my own investigating and found this page ( from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2263411 ) that lists all probes on the microarray platform used by the authors. All probe IDs have the prefix *Cust* and it appears to be a random name assingment. For *CUST_735_PI427 ...
written 6 days ago by Kevin Blighe11k
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Comment: C: bcftools merge failed: incorrect number of PL fields
... It was just a way of making sure that other issues unrelated to the PL were not the cause. Sometimes error messages are hopelessly unhelpful. glad that you got it sorted. ...
written 6 days ago by Kevin Blighe11k
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Answer: A: Compare genotypes between WGS and Targeted pannel
... You should: 1. filter the datasets so that only common variants are included 2. Normalise the VCFS / BCFs (`bcftools norm -m-any`) 3. merge everything together 4. Read the data into PLINK and check samples against 1000 genomes ( see https://www.biostars.org/p/271694/ ) 5. Run the comparis ...
written 6 days ago by Kevin Blighe11k

Latest awards to Kevin Blighe

Appreciated 20 hours ago, created a post with more than 5 votes. For A: pathogenicity predictors of cancer mutations
Teacher 20 hours ago, created an answer with at least 3 up-votes. For A: Compare two columns of same file as paired rows
Scholar 20 hours ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Commentator 4 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
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Commentator 7 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
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Scholar 10 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
Scholar 10 days ago, created an answer that has been accepted. For A: Compare two columns of same file as paired rows
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