Moderator: Jorge Amigo
Jorge Amigo ♦ 11k
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Scrutinizing genomic human variation by dealing with high throughput genotyping and next generation sequencing results, among many other things.
Posts by Jorge Amigo
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... It doesn't exactly answer your question, but if you're dealing with regions you may want to have a look to `bedtools`:
$ bedtools intersect -a file1.bed -b file2.bed -wa
SpoScf_15890 12 2376
SpoScf_07684 10 4075
SpoScf_07684 64 4276
Super_scaffold_60 ...
written 8 weeks ago by
Jorge Amigo ♦ 11k
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Comment:
C: How to count fastq reads
... the only very slight problem I see is that very rare 1 base sequences (trimmed perhaps) with "+" quality would be counted twice, but I love the simplicity of this answer. ...
written 4 months ago by
Jorge Amigo ♦ 11k
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... although chr1 is one of the biggest ones, and considering that you've already done the largest effort which is calling variants on NA12878, I'd definitely go for the entire genome's numbers rather than being fine with a relatively small subset of statistics. ...
written 6 months ago by
Jorge Amigo ♦ 11k
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... you've chosen a reference sample to apply your variant calling pipeline to. well done, because you're almost there. just get a set of [high confidence NA12878 variants][1] such as the [GiB project][2] ones, use a comparison tool such as [RTG vcfeval][3] (the one recommended by the [GiB project][4]), ...
written 6 months ago by
Jorge Amigo ♦ 11k
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... it's difficult to say anything without knowing the content of your VCF file, but here are a couple of suggestions:
1. have you checked your VCF and your BED files refer to the same reference? one quick dirty check is making sure that you're either using or not using in both files the "chr" prefix, ...
written 6 months ago by
Jorge Amigo ♦ 11k
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... you should check if IGV is filtering any kind of reads. typically this is caused by IGV's default duplicate reads filtering.
just unselect everything you see under "View > Preferences > Alignments > Filter..." and you should see in IGV's coverage track the same profile than the Bedgraph ha ...
written 6 months ago by
Jorge Amigo ♦ 11k
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... if you already have exome data from each parent, if you have aligned it, and you have called variants, then you would have already ended up with 2 bam files and 2 vcf files.
if you need now to compare variants among them you don't have to map them again. you just have to compare the vcf files you a ...
written 8 months ago by
Jorge Amigo ♦ 11k
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... sorting such a big file only for being able to use the uniq function wouldn't be the more efficient way to do it, plus a simple `sort -u` wouldn't address the problem described in the question as the lines that need to be merged/skipped do vary. if sorting would be considered (and it would be really ...
written 8 months ago by
Jorge Amigo ♦ 11k
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... this is the same as an uniq function on entire lines, and it doesn't work with your example considering that positions qualities vary from line to line. you need to group (index) only the columns you expect to be repeated, as explained in the example I suggested previously. ...
written 8 months ago by
Jorge Amigo ♦ 11k
3
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... I don't know of a direct method to accomplish what you need, but have a look at this tentative proposal:
awk 'FS=OFS="\t"{print $1, 0, $2}' human_hg19.fa.fai \
| bedtools makewindows -b - -w 1000 \
| bedtools map -a - -b input.bedgraph -c 4 -o sum \
| grep -P "\d$"
what it does is: ...
written 8 months ago by
Jorge Amigo ♦ 11k
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