User: ellieuk

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ellieuk10
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Posts by ellieuk

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Making a new header depending on entries from old header
... For many this will be very basic, but for me it's driving me nuts! I have a tab-delimited header: ``` sampleA sampleB sampleC ``` Depending on the number of samples I have, I want to make a new header as such: For 3 samples: ``` sampleA sampleB sampleC output001 output002 output003 ``` For 4 sam ...
unix written 8 weeks ago by ellieuk10
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Comment: C: Calculate gene % covered at depth X
... Thanks for the response. That doesn’t work because I need to only count a gene as covered when the read depth is 10x at any position across that gene. ...
written 3 months ago by ellieuk10
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Calculate gene % covered at depth X
... Hi, I'd like to calculate the percentage of given genes covered by an aligned BAM at a given depth i.e. 10x. Output expected: Gene_name percentage_covered_at_10x Gene1 95% Gene2 80% Gene3 99% I tried: `bedtools coverage -abam input. ...
genome bedtools alignment written 4 months ago by ellieuk10 • updated 3 months ago by zx87549.6k
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... Will do. As an addition (in case it helps for anyone else) I've been working on an alternative solution using a perl script. A further option would be to use: convert2annovar.pl -format vcf4 example/ex2.vcf -outfile ex2 -allsample That will add zygosities and split a multi-sample vcf into indi ...
written 4 months ago by ellieuk10
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... Thanks you very much, worked beautifully! ...
written 4 months ago by ellieuk10
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... *laughing emoji* I can use R, but my student can't! ...
written 4 months ago by ellieuk10
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... Hi Pierre, Thanks for your response. The problem is that this doesn’t work for the student I’m supervising who can’t use the command line. They need to work on a flat csv file such as in excel to filter on inheritance patterns. We need a multi-sample Annovar output that includes all variants as het ...
written 4 months ago by ellieuk10
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... I want to be able to filter for all! We don’t know. It could be de novo, dominant and with incomplete penetrance, recessive, X linked etc. The idea is that I can filter for all inheritance patterns if I have the ref/het/hom for all individuals simply laid out in one single annotated file. ...
written 4 months ago by ellieuk10
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... Hi Pierre, I’m trying to get an annotated annovar file that includes all samples (mum, dad, and proband) but instead of having the genotypes as 1/1, 1/0, 0/0 etc, I would like 3 columns for mum, dad, and proband in the same file but with het, hom or ref. Currently annovar allows you to print zygosi ...
written 4 months ago by ellieuk10
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Phasing a trio in multi-sample vcf with zygosity
... Hi there, I'd be grateful for some help please. I've got several joint-called trio VCFs (unaffected parents and proband) which I'm analysing. The multi-sample vcf nicely shows 0/0, 0/1, 1/1 for each individual per variant. However, I'd like to convert the notation to three columns of simply het, h ...
genome written 4 months ago by ellieuk10 • updated 4 months ago by Pierre Lindenbaum130k

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