User: flutabex

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flutabex30
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Posts by flutabex

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Could you help me set up a VCF filter?
... Ah, sorry, I didn't realise that would cause difficulties. The GRCh38 VCFs I've already got include the LongRanger files and also a few others from a different pipeline (possibly GATK?), but I think he did do some things slightly differently from usual to work better with the chromium data. Yes, i ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... Hello again, one more quick question before I open the new post: I've run bamtofastq with just the default command - would it be worth running it again with any of the options, e.g. -fq2? My sequence is from chromium 10x linked read. Thanks again for your help. ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... Thank you, that's really helpful. I'm just working out how to use bamtofastq then will open a new question as you suggest. I *will* get there! ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... Lol it had occurred to me that if I really couldn't get anywhere I might have to resort to excel, but it'd be a very long, tedious, error-prone process. I haven't explained very well, but the initial couple of genes are only the first step. Even if I do have clear evidence of the most strongly indic ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... I actually already have the BAM file so it'd be great if you could show me how to re-align from that. Re interpretation, my plan was to first see if I have any of the known pathogenic mutations in the genes most strongly implicated by the clinical presentation. There is a fairly strong suspicion of ...
written 4 months ago by flutabex30
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Comment: A: Could you help me set up a VCF filter?
... Hi, thank you and sorry for slow reply - I'm not well and can't always use the computer. I said either liftover or realign because I thought you had said it might be possible to take it back to fastq and align to GRCh37 myself, if my computer could handle it. I may well have misunderstood that thou ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... Hi, don't know if you're around today... do you think I might be able to realign the VCF myself? I've been trying LiftoverVCF again, this time in Ubuntu on the Windows Subsystem for Linux, but just keep getting errors and don't know enough linux or java to know what I'm doing wrong. ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... Sorry for delayed reply - I'd reached the posting limit as a new member so it wouldn't let me post again last night. 3 or 4 genes are main priority, then another 10 or so, then quite a few more "possibles". I'd like to practise anything new with a particular gene where I already know some of the v ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... That's right, also on predicted impact. My computer is a 2 year old Thinkpad, Intel i7-5600U CPU @ 2.60GHz, 12 GB RAM. Could that cope with alignment do you think? ...
written 4 months ago by flutabex30
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Comment: C: Could you help me set up a VCF filter?
... Ah, thanks for checking that out, saved me a lot of time. I didn't do the alignment, only have the files and would probably have to pay to get them redone. If I can't get anywhere fairly soon I shall ask anyway though - it's so frustrating to have the data and not be able to analyse it. ...
written 4 months ago by flutabex30

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