User: JSEM

gravatar for JSEM
JSEM20
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New User
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2 months, 3 weeks ago
Joined:
5 months, 1 week ago
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Posts by JSEM

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Updating allele frequency (AF) and minor allele frequency (MAF) INFO fields in .
... Thanks for the quick reply. This approach seems like it should be quite straightforward, difficulty is that I'm running this on an HPC cluster, where running java programs is not very straightforward given permissions...etc and modules available on HPC. Are there any other approaches that are non- ...
written 3 months ago by JSEM20
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Updating allele frequency (AF) and minor allele frequency (MAF) INFO fields in .vcf
... Hi everyone, I'm processing .vcf files for the first time, and am hoping for some advice with something. I recently filtered a set of .VCFs for a dataset to exclude around half of the subjects, but now want to update the INFO columns in me output files to reflect the stats of the new filtered datas ...
vcf imputation qc vcftools snp written 3 months ago by JSEM20
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Picard liftoverVCF error when attempting to liftover to build 38
... Hi, I've been trying to lift over .vcf files (human) from build 37 to build 38 using Picard's lftoverVCF. After some very helpful tips from other BioStars users (reference fasta file has been appropriately indexed, I'm also running the latest version of Picard (2.17.3)), I'm now at the stage where ...
genome assembly sequence snp software error written 5 months ago by JSEM20 • updated 22 days ago by dariober9.2k
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Comment: C: Liftover of .vcf files from build 37 to build 38
... Hello JSEM! We believe that this post does not fit the main topic of this site. This issue solved. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be ...
written 5 months ago by JSEM20
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Comment: C: Liftover of .vcf files from build 37 to build 38
... Ah, OK, thanks! First time posting so didn't realise a separate post was needed. ...
written 5 months ago by JSEM20
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Comment: C: Liftover of .vcf files from build 37 to build 38
... Hi again, I've now upgraded Picard, and indexed the reference fasta file, which seems to have solved the first error I was encountering. I now seem to have an error relating to the header in the vcf file (original produced by the Michigan Imputation Server, and subsequently thinned down using vcfto ...
written 5 months ago by JSEM20
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Comment: C: Liftover of .vcf files from build 37 to build 38
... Have just tried to do this. Will give it a go and update here. Thanks for the suggestion! ...
written 5 months ago by JSEM20
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Comment: C: Liftover of .vcf files from build 37 to build 38
... Actually probably not, I wasn't aware it needed to be (blush). Thanks, will try this. ...
written 5 months ago by JSEM20
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Comment: C: Liftover of .vcf files from build 37 to build 38
... Thanks for the quick reply! I've now upgraded to the latest Picard (2.17.3), so will try with that and see ...
written 5 months ago by JSEM20
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(Closed) Liftover of .vcf files from build 37 to build 38
... Hi, I'm hoping someone may have some pearls of wisdom. I've been trying to liftover .vcf files (human) from build 37 to build 38, and have tried a variety of different approaches, none of which have worked so far. NCBI's web tool produces an error stating that I am trying to access a page I do not ...
genome sequence snp written 5 months ago by JSEM20 • updated 5 months ago by Hussain Ather860

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