User: ekwame
ekwame • 60
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Posts by ekwame
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... thanks @genomax for the explanation. yes it seems these genes are also in the patches.
what is usually done in the community? these are list of DNA repair genes which i want to the intersect with my `.VCFs`
any suggestions on how to go about this correctly? ...
written 5 weeks ago by
ekwame • 60
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... Hi all,
i download few ensensemble genes with cordinates (Human genes (GRCh38.p13)) from biomart and want to convert to ucsc hg38 cordinates.
there are some contigs not in hg38 ref dictionary
see this example (full file below);
CHR_HSCHR5_1_CTG1_1 70376388 70411404 ENSG00000276910 GTF2H2
i did ...
written 5 weeks ago by
ekwame • 60
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... Specifying an interval list restricts your variant calling to only regions in the interval list. by not specifying an interval list, you are calling variants across the whole genome hence the big size of your output file. interval list are particularly useful when for whole exomes sequence data whe ...
written 6 weeks ago by
ekwame • 60
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... Hi
I'm using annovar to filter germline variants by `--score_threshold` but nothing is either filtered or dropped.
please I'm I missing something in the code?
`perl annotate_variation.pl --filter /sc/hydra/projects/canan/Breast_Cancer/results/germline/new_germline07302020/Germline_108_07302020.vc ...
written 6 weeks ago by
ekwame • 60
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... Thanks @Kevin Blighe,
it turns out the 'strand' column was the source of error. i think because of `ignore.strand=TRUE` flag in `GenomicRanges::makeGRangesFromDataFrame`
set `ignore.strand=TRUE` inistially because `GenomicRanges::makeGRangesFromDataFrame` wasn't recognizing values in `strand` colu ...
written 3 months ago by
ekwame • 60
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... class(merged.biomart.hg19.cna)
[1] "data.frame"
typeof(merged.biomart.hg19.cna)
[1] "list"
str(merged.biomart.hg19.cna)
'data.frame': 57812 obs. of 24 variables:
$ seqnames : Factor w/ 24 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
$ start ...
written 3 months ago by
ekwame • 60
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... Hello Biostars,
converting dataframe to Granges object using `GenomicRanges::makeGRangesFromDataFrame` but keeeps failing due to presumably reserved names in metadata column
but my metadata columns do not contain these
"seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "s ...
written 3 months ago by
ekwame • 60
• updated
3 months ago by
Kevin Blighe ♦ 65k
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... ouch! I forget to post my solution!
just in case someone else encounters similar solution.
`bcftools reheader --samples` requires a file with sample names so I specified correctly file in local directory by inserting quotes `"${sampleName}.txt"` to make it work.
thanks everyone for the support
S
...
written 3 months ago by
ekwame • 60
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... Dear Biostars,
I have GRangesList object of length 15 with metadata (of gene annotations & copy number),
created small GRanges object to use to query GrangeList by subsetByOverlaps. but subsetByOverlaps seem not working for GrnagesLists, results end being same as orginial GrangesList.
has anyon ...
written 3 months ago by
ekwame • 60
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... I tried this second approach but results are printed to the screen;
I'm not really sure what I'm doing wrong?
gvcfs="/sc/hydra/projects/canan/colon_cancer10312019/joint_calling_colon/gvcfs/renamed_sm_gvcfs/*.hg38.g.vcf.gz"
for i in $gvcfs
do
sampleName=`basename -s .hg38.g.vcf.gz ...
written 5 months ago by
ekwame • 60
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