User: joangibert14

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Posts by joangibert14

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Answer: A: Modify IOT formated VCF by the most frequent variant
... I kind of solve it using vcfR package. If anyone would need to do this in the future, here is the issue: https://github.com/knausb/vcfR/issues/112 ...
written 8 weeks ago by joangibert140
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Comment: C: Modify IOT formated VCF by the most frequent variant
... Thanks for your help! As you may suppose, managing vcf files is quite new to me... Here's an input example: https://gist.github.com/Tato14/ce1f2ab9c38c63a201ba1756a5e20dd8 ...
written 9 weeks ago by joangibert140
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Comment: C: Modify IOT formated VCF by the most frequent variant
... Hi Pierre! Thanks for the formatting. > I would like to get rid of the rest of the variants. Means that I only want to keep only one COSMIC ALT allele (the one with bigger AF). I wasn't aware of the `Number=A`. Here's an output example: CHROM POS ID REF ALT QUAL FILTER INFO FO ...
written 9 weeks ago by joangibert140
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Modify IOT formated VCF by the most frequent variant
... I have a VCF from the IOT server analyzer which look like (I paste just one entry for a call of a variant in KRAS gene): CHROM POS ID REF ALT QUAL FILTER INFO FORMAT chr12 25398280 COSM536;COSM535;COSM12655;COSM537;COSM12721;COSM531;COSM87280;COSM532;COSM528;COSM523;COSM521;COSM25081;COS ...
vcf R snp bash written 10 weeks ago by joangibert140
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Comment: C: Remove entries in a IRangesList
... Hi! Thanks! It worked for me without the `unlist` function. And yes, `` gives the chromosome information :). ...
written 10 weeks ago by joangibert140
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Remove entries in a IRangesList
... Hi! I have an IRangesList with several entries like: [[1]] IRanges object with 1 range and 8 metadata columns: start end width | tx_id cds_ok exon_id exon_rank seq_start seq_end | -1 -1 1 | ENST ...
R written 10 weeks ago by joangibert140 • updated 10 weeks ago by ATpoint7.5k
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Comment: C: Get aminoacid sequence and position from genomic coordinates
... Hello Fin, I have the reference fasta (GRCh37) and the annotation file (in this case refGene). Also, I know which gene corresponds the region but this could change between samples so I don't know if this should be strictly necessary. Thanks for your help :) J ...
written 12 weeks ago by joangibert140
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Get aminoacid sequence and position from genomic coordinates
... Hi! I have some coordinates bellow a given coverage from DNA seq experiments. Something like : chr2 212578373 212578415 I would like to obtain the genomic sequence, the protein position with the exon information (although I think I solved this: https://doi.org/doi:10.18129/B9.bioc.ensembldb ) ...
sequence written 12 weeks ago by joangibert140 • updated 11 weeks ago by genomax55k
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Comment: C: Fill a VCF record field that is partially annotated
... It works great! Thanks! Also, if there is more than one ALT allele and they are separated with commas (,) there is no problem with this command :) ...
written 3 months ago by joangibert140
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Fill a VCF record field that is partially annotated
... I have a VCF like: chr1 65310489 . T C 3483.8 PASS AF=0.476857;AO=441;DP=931;FAO=443;FDP=929;FDVR=5 [...] AF_gnomAD=0.353 [...] chr1 65310518 . A T 96.8 PASS AF=0.00107066;AO=1;DP=934;FAO=1;FDP=934;FDVR=10 [...] ... Where I added an extra field with the AF using the gnomAD database ...
vcf vcfanno gnomad snp written 3 months ago by joangibert140 • updated 3 months ago by Pierre Lindenbaum112k

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Scholar 8 weeks ago, created an answer that has been accepted. For A: Modify IOT formated VCF by the most frequent variant

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